mirror of
https://github.com/msberends/AMR.git
synced 2025-07-27 14:27:53 +02:00
Built site for AMR: 2.0.0.9028@3829311
This commit is contained in:
github-actions
@ -10,7 +10,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9026</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9028</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">
|
||||
@ -170,24 +170,52 @@
|
||||
|
||||
<div class="section level2">
|
||||
<h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2>
|
||||
<p>A <a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble</a> with 42 599 observations and 12 variables:</p><ul><li><p><code>guideline</code><br> Name of the guideline</p></li>
|
||||
<li><p><code>method</code><br> Either "DISK" or "MIC"</p></li>
|
||||
<li><p><code>site</code><br> Body site, e.g. "Oral" or "Respiratory"</p></li>
|
||||
<p>A <a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble</a> with 28 454 observations and 12 variables:</p><ul><li><p><code>guideline</code><br> Name of the guideline</p></li>
|
||||
<li><p><code>type</code><br> Breakpoint type, either "ECOFF", "animal", or "human"</p></li>
|
||||
<li><p><code>method</code><br> Testing method, either "DISK" or "MIC"</p></li>
|
||||
<li><p><code>site</code><br> Body site for which the breakpoint must be applied, e.g. "Oral" or "Respiratory"</p></li>
|
||||
<li><p><code>mo</code><br> Microbial ID, see <code><a href="as.mo.html">as.mo()</a></code></p></li>
|
||||
<li><p><code>rank_index</code><br> Taxonomic rank index of <code>mo</code> from 1 (subspecies/infraspecies) to 5 (unknown microorganism)</p></li>
|
||||
<li><p><code>ab</code><br> Antibiotic ID, see <code><a href="as.ab.html">as.ab()</a></code></p></li>
|
||||
<li><p><code>ab</code><br> Antibiotic code as used by this package, EARS-Net and WHONET, see <code><a href="as.ab.html">as.ab()</a></code></p></li>
|
||||
<li><p><code>ref_tbl</code><br> Info about where the guideline rule can be found</p></li>
|
||||
<li><p><code>disk_dose</code><br> Dose of the used disk diffusion method</p></li>
|
||||
<li><p><code>breakpoint_S</code><br> Lowest MIC value or highest number of millimetres that leads to "S"</p></li>
|
||||
<li><p><code>breakpoint_R</code><br> Highest MIC value or lowest number of millimetres that leads to "R"</p></li>
|
||||
<li><p><code>ecoff</code><br> Epidemiological cut-off (ECOFF) value, used in antimicrobial susceptibility testing to differentiate between wild-type and non-wild-type strains of bacteria or fungi (use <code><a href="as.sir.html">as.sir(..., ecoff = TRUE)</a></code> to interpret raw data using ECOFF values)</p></li>
|
||||
<li><p><code>uti</code><br> A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> value (<code>TRUE</code>/<code>FALSE</code>) to indicate whether the rule applies to a urinary tract infection (UTI)</p></li>
|
||||
</ul></div>
|
||||
<div class="section level2">
|
||||
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
|
||||
<p>Clinical breakpoints are validated through <a href="https://whonet.org" class="external-link">WHONET</a>, a free desktop Windows application developed and supported by the WHO Collaborating Centre for Surveillance of Antimicrobial Resistance. More can be read on <a href="https://whonet.org" class="external-link">their website</a>.</p>
|
||||
<p>Like all data sets in this package, this data set is publicly available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, and Stata. Please visit <a href="https://msberends.github.io/AMR/articles/datasets.html">our website for the download links</a>. The actual files are of course available on <a href="https://github.com/msberends/AMR/tree/main/data-raw" class="external-link">our GitHub repository</a>.</p>
|
||||
<p>They <strong>allow for machine reading EUCAST and CLSI guidelines</strong>, which is almost impossible with the MS Excel and PDF files distributed by EUCAST and CLSI.</p>
|
||||
|
||||
<div class="section">
|
||||
<h3 id="different-types-of-breakpoints">Different types of breakpoints<a class="anchor" aria-label="anchor" href="#different-types-of-breakpoints"></a></h3>
|
||||
|
||||
|
||||
<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>
|
||||
</div>
|
||||
|
||||
<div class="section">
|
||||
<h3 id="imported-from-whonet">Imported from WHONET<a class="anchor" aria-label="anchor" href="#imported-from-whonet"></a></h3>
|
||||
|
||||
|
||||
<p>Clinical breakpoints in this package were validated through and imported from <a href="https://whonet.org" class="external-link">WHONET</a>, a free desktop Windows application developed and supported by the WHO Collaborating Centre for Surveillance of Antimicrobial Resistance. More can be read on <a href="https://whonet.org" class="external-link">their website</a>. The developers of WHONET and this <code>AMR</code> package have been in contact about sharing their work. We highly appreciate their development on the WHONET software.</p>
|
||||
</div>
|
||||
|
||||
<div class="section">
|
||||
<h3 id="response-from-clsi-and-eucast">Response from CLSI and EUCAST<a class="anchor" aria-label="anchor" href="#response-from-clsi-and-eucast"></a></h3>
|
||||
|
||||
|
||||
<p>The CEO of CLSI and the chairman of EUCAST have endorsed the work and public use of this <code>AMR</code> package in June 2023, when future development of distributing clinical breakpoints was discussed in a meeting between CLSI, EUCAST, the WHO, and developers of WHONET and the <code>AMR</code> package.</p>
|
||||
</div>
|
||||
|
||||
<div class="section">
|
||||
<h3 id="download">Download<a class="anchor" aria-label="anchor" href="#download"></a></h3>
|
||||
|
||||
|
||||
<p>Like all data sets in this package, this data set is publicly available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, and Stata. Please visit <a href="https://msberends.github.io/AMR/articles/datasets.html">our website for the download links</a>. The actual files are of course available on <a href="https://github.com/msberends/AMR/tree/main/data-raw" class="external-link">our GitHub repository</a>. They allow for machine reading EUCAST and CLSI guidelines, which is almost impossible with the MS Excel and PDF files distributed by EUCAST and CLSI, though initiatives have started to overcome these burdens.</p>
|
||||
<p><strong>NOTE:</strong> this <code>AMR</code> package (and the WHONET software as well) contains internal methods to apply the guidelines, which is rather complex. For example, some breakpoints must be applied on certain species groups (which are in case of this package available through the <a href="microorganisms.groups.html">microorganisms.groups</a> data set). It is important that this is considered when using the breakpoints for own use.</p>
|
||||
</div>
|
||||
|
||||
</div>
|
||||
<div class="section level2">
|
||||
<h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
|
||||
@ -197,22 +225,21 @@
|
||||
<div class="section level2">
|
||||
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
|
||||
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">clinical_breakpoints</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 42,599 × 12</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> guideline method site mo rank_index ab ref_tbl disk_dose</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><ab></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> EUCAST 2023 MIC <span style="color: #BB0000;">NA</span> F_ASPRG_MGTS 2 AMB Aspergillus <span style="color: #BB0000;">NA</span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> EUCAST 2023 MIC <span style="color: #BB0000;">NA</span> F_ASPRG_NIGR 2 AMB Aspergillus <span style="color: #BB0000;">NA</span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> EUCAST 2023 MIC <span style="color: #BB0000;">NA</span> F_CANDD_ALBC 2 AMB Candida <span style="color: #BB0000;">NA</span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> EUCAST 2023 MIC <span style="color: #BB0000;">NA</span> F_CANDD_DBLN 2 AMB Candida <span style="color: #BB0000;">NA</span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> EUCAST 2023 MIC <span style="color: #BB0000;">NA</span> F_CANDD_GLBR 2 AMB Candida <span style="color: #BB0000;">NA</span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> EUCAST 2023 MIC <span style="color: #BB0000;">NA</span> F_CANDD_KRUS 2 AMB Candida <span style="color: #BB0000;">NA</span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> EUCAST 2023 MIC <span style="color: #BB0000;">NA</span> F_CANDD_PRPS 2 AMB Candida <span style="color: #BB0000;">NA</span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> EUCAST 2023 MIC <span style="color: #BB0000;">NA</span> F_CANDD_TRPC 2 AMB Candida <span style="color: #BB0000;">NA</span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> EUCAST 2023 MIC <span style="color: #BB0000;">NA</span> F_CRYPT_NFRM 2 AMB Candida <span style="color: #BB0000;">NA</span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> EUCAST 2023 MIC <span style="color: #BB0000;">NA</span> B_ANAER-NEG 6 AMC Gram-negativ… <span style="color: #BB0000;">NA</span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 42,589 more rows</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 4 more variables: breakpoint_S <dbl>, breakpoint_R <dbl>, ecoff <dbl>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># uti <lgl></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 28,454 × 12</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> guideline type method site mo rank_index ab ref_tbl disk_dose</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><ab></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> EUCAST 2… human DISK <span style="color: #BB0000;">NA</span> B_ACHRMB_DNTR 2 MEM A. xylo… 10ug </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> EUCAST 2… human MIC <span style="color: #BB0000;">NA</span> B_ACHRMB_DNTR 2 MEM A. xylo… <span style="color: #BB0000;">NA</span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> EUCAST 2… human DISK <span style="color: #BB0000;">NA</span> B_ACHRMB_DNTR 2 SXT A. xylo… 1.25ug/2…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> EUCAST 2… human MIC <span style="color: #BB0000;">NA</span> B_ACHRMB_DNTR 2 SXT A. xylo… <span style="color: #BB0000;">NA</span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> EUCAST 2… human DISK <span style="color: #BB0000;">NA</span> B_ACHRMB_DNTR 2 TZP A. xylo… 30ug/6ug </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> EUCAST 2… human MIC <span style="color: #BB0000;">NA</span> B_ACHRMB_DNTR 2 TZP A. xylo… <span style="color: #BB0000;">NA</span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> EUCAST 2… human DISK <span style="color: #BB0000;">NA</span> B_ACHRMB_XYLS 2 MEM A. xylo… 10ug </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> EUCAST 2… human MIC <span style="color: #BB0000;">NA</span> B_ACHRMB_XYLS 2 MEM A. xylo… <span style="color: #BB0000;">NA</span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> EUCAST 2… human DISK <span style="color: #BB0000;">NA</span> B_ACHRMB_XYLS 2 SXT A. xylo… 1.25ug/2…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> EUCAST 2… human MIC <span style="color: #BB0000;">NA</span> B_ACHRMB_XYLS 2 SXT A. xylo… <span style="color: #BB0000;">NA</span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 28,444 more rows</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 3 more variables: breakpoint_S <dbl>, breakpoint_R <dbl>, uti <lgl></span></span>
|
||||
</code></pre></div>
|
||||
</div>
|
||||
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
|
||||
|
||||
Reference in New Issue
Block a user