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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</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="">2.1.1.9270</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9272</small>
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@ -424,19 +424,19 @@ column names:<br><em>ab</em>, <em>cid</em>, <em>name</em>, <em>group</em>, <em>a
<em>iv_ddd</em>, <em>iv_units</em>, and <em>loinc</em>.</p> <em>iv_ddd</em>, <em>iv_units</em>, and <em>loinc</em>.</p>
<p>This data set is in R available as <code>antimicrobials</code>, after <p>This data set is in R available as <code>antimicrobials</code>, after
you load the <code>AMR</code> package.</p> you load the <code>AMR</code> package.</p>
<p>It was last updated on 4 May 2025 12:24:43 UTC. Find more info about <p>It was last updated on 4 May 2025 14:38:09 UTC. Find more info about
the contents, (scientific) source, and structure of this <a href="https://amr-for-r.org/reference/antimicrobials.html">data set the contents, (scientific) source, and structure of this <a href="https://amr-for-r.org/reference/antimicrobials.html">data set
here</a>.</p> here</a>.</p>
<p><strong>Direct download links:</strong></p> <p><strong>Direct download links:</strong></p>
<ul> <ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/datasets/antimicrobials.rds" class="external-link">original <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/datasets/antimicrobials.rds" class="external-link">original
R Data Structure (RDS) file</a> (44 kB)<br> R Data Structure (RDS) file</a> (45 kB)<br>
</li> </li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/datasets/antimicrobials.txt" class="external-link">tab-separated <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/datasets/antimicrobials.txt" class="external-link">tab-separated
text file</a> (0.1 MB)<br> text file</a> (0.1 MB)<br>
</li> </li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/datasets/antimicrobials.xlsx" class="external-link">Microsoft <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/datasets/antimicrobials.xlsx" class="external-link">Microsoft
Excel workbook</a> (77 kB)<br> Excel workbook</a> (78 kB)<br>
</li> </li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/datasets/antimicrobials.feather" class="external-link">Apache <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/datasets/antimicrobials.feather" class="external-link">Apache
Feather file</a> (0.1 MB)<br> Feather file</a> (0.1 MB)<br>
@ -512,7 +512,7 @@ as comma separated values.</p>
<td align="center">J01CA04, QG51AA03, QJ01CA04</td> <td align="center">J01CA04, QG51AA03, QJ01CA04</td>
<td align="center">Beta-lactam antibacterials, penicillins</td> <td align="center">Beta-lactam antibacterials, penicillins</td>
<td align="center">Penicillins with extended spectrum</td> <td align="center">Penicillins with extended spectrum</td>
<td align="center">ac, amox, amx</td> <td align="center">ac, amox, amoxic, …</td>
<td align="center">acuotricina, alfamox, alfida, …</td> <td align="center">acuotricina, alfamox, alfida, …</td>
<td align="center">1.5</td> <td align="center">1.5</td>
<td align="center">g</td> <td align="center">g</td>
@ -545,7 +545,7 @@ inhibitors</td>
<td align="center">J01CA01, QJ01CA01, QJ51CA01, …</td> <td align="center">J01CA01, QJ01CA01, QJ51CA01, …</td>
<td align="center">Beta-lactam antibacterials, penicillins</td> <td align="center">Beta-lactam antibacterials, penicillins</td>
<td align="center">Penicillins with extended spectrum</td> <td align="center">Penicillins with extended spectrum</td>
<td align="center">am, amp, ampi</td> <td align="center">am, amp, amp100, …</td>
<td align="center">adobacillin, alpen, amblosin, …</td> <td align="center">adobacillin, alpen, amblosin, …</td>
<td align="center">2.0</td> <td align="center">2.0</td>
<td align="center">g</td> <td align="center">g</td>
@ -1794,35 +1794,35 @@ set here</a>.</p>
<h2 id="microorganisms-codes-common-laboratory-codes"> <h2 id="microorganisms-codes-common-laboratory-codes">
<code>microorganisms.codes</code>: Common Laboratory Codes<a class="anchor" aria-label="anchor" href="#microorganisms-codes-common-laboratory-codes"></a> <code>microorganisms.codes</code>: Common Laboratory Codes<a class="anchor" aria-label="anchor" href="#microorganisms-codes-common-laboratory-codes"></a>
</h2> </h2>
<p>A data set with 5 063 rows and 2 columns, containing the following <p>A data set with 6 036 rows and 2 columns, containing the following
column names:<br><em>code</em> and <em>mo</em>.</p> column names:<br><em>code</em> and <em>mo</em>.</p>
<p>This data set is in R available as <code>microorganisms.codes</code>, <p>This data set is in R available as <code>microorganisms.codes</code>,
after you load the <code>AMR</code> package.</p> after you load the <code>AMR</code> package.</p>
<p>It was last updated on 20 April 2025 13:27:36 UTC. Find more info <p>It was last updated on 4 May 2025 16:50:25 UTC. Find more info about
about the contents, (scientific) source, and structure of this <a href="https://amr-for-r.org/reference/microorganisms.codes.html">data the contents, (scientific) source, and structure of this <a href="https://amr-for-r.org/reference/microorganisms.codes.html">data
set here</a>.</p> set here</a>.</p>
<p><strong>Direct download links:</strong></p> <p><strong>Direct download links:</strong></p>
<ul> <ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/datasets/microorganisms.codes.rds" class="external-link">original <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/datasets/microorganisms.codes.rds" class="external-link">original
R Data Structure (RDS) file</a> (23 kB)<br> R Data Structure (RDS) file</a> (27 kB)<br>
</li> </li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/datasets/microorganisms.codes.txt" class="external-link">tab-separated <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/datasets/microorganisms.codes.txt" class="external-link">tab-separated
text file</a> (0.1 MB)<br> text file</a> (0.1 MB)<br>
</li> </li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/datasets/microorganisms.codes.xlsx" class="external-link">Microsoft <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/datasets/microorganisms.codes.xlsx" class="external-link">Microsoft
Excel workbook</a> (84 kB)<br> Excel workbook</a> (98 kB)<br>
</li> </li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/datasets/microorganisms.codes.feather" class="external-link">Apache <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/datasets/microorganisms.codes.feather" class="external-link">Apache
Feather file</a> (87 kB)<br> Feather file</a> (0.1 MB)<br>
</li> </li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/datasets/microorganisms.codes.parquet" class="external-link">Apache <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/datasets/microorganisms.codes.parquet" class="external-link">Apache
Parquet file</a> (59 kB)<br> Parquet file</a> (68 kB)<br>
</li> </li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/datasets/microorganisms.codes.sav" class="external-link">IBM <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/datasets/microorganisms.codes.sav" class="external-link">IBM
SPSS Statistics data file</a> (0.1 MB)<br> SPSS Statistics data file</a> (0.2 MB)<br>
</li> </li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/datasets/microorganisms.codes.dta" class="external-link">Stata <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/datasets/microorganisms.codes.dta" class="external-link">Stata
DTA file</a> (0.1 MB)</li> DTA file</a> (0.2 MB)</li>
</ul> </ul>
<p><strong>Example content</strong></p> <p><strong>Example content</strong></p>
<table class="table"> <table class="table">

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@ -33,7 +33,7 @@
<a class="navbar-brand me-2" href="index.html">AMR (for R)</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="">2.1.1.9270</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9272</small>
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</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="">2.1.1.9270</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9272</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"> <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>
<div class="section level2"> <div class="section level2">
<h2 class="pkg-version" data-toc-text="2.1.1.9270" id="amr-2119270">AMR 2.1.1.9270<a class="anchor" aria-label="anchor" href="#amr-2119270"></a></h2> <h2 class="pkg-version" data-toc-text="2.1.1.9272" id="amr-2119272">AMR 2.1.1.9272<a class="anchor" aria-label="anchor" href="#amr-2119272"></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><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> <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"> <div class="section level3">
<h3 id="tldr-2-1-1-9270">tl;dr<a class="anchor" aria-label="anchor" href="#tldr-2-1-1-9270"></a></h3> <h3 id="tldr-2-1-1-9272">tl;dr<a class="anchor" aria-label="anchor" href="#tldr-2-1-1-9272"></a></h3>
<ul><li>Scope Expansion: One Health support (Human + Veterinary + Environmental microbiology).</li> <ul><li>Scope Expansion: One Health support (Human + Veterinary + Environmental microbiology).</li>
<li>Data Updates: <li>Data Updates:
<ul><li> <ul><li>
@ -103,15 +103,15 @@
</ul></li> </ul></li>
</ul></div> </ul></div>
<div class="section level3"> <div class="section level3">
<h3 id="full-changelog-2-1-1-9270">Full Changelog<a class="anchor" aria-label="anchor" href="#full-changelog-2-1-1-9270"></a></h3> <h3 id="full-changelog-2-1-1-9272">Full Changelog<a class="anchor" aria-label="anchor" href="#full-changelog-2-1-1-9272"></a></h3>
<div class="section level4"> <div class="section level4">
<h4 id="breaking-2-1-1-9270">Breaking<a class="anchor" aria-label="anchor" href="#breaking-2-1-1-9270"></a></h4> <h4 id="breaking-2-1-1-9272">Breaking<a class="anchor" aria-label="anchor" href="#breaking-2-1-1-9272"></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> <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>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> <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> </ul></div>
<div class="section level4"> <div class="section level4">
<h4 id="new-2-1-1-9270">New<a class="anchor" aria-label="anchor" href="#new-2-1-1-9270"></a></h4> <h4 id="new-2-1-1-9272">New<a class="anchor" aria-label="anchor" href="#new-2-1-1-9272"></a></h4>
<ul><li> <ul><li>
<strong>One Health implementation</strong> <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> <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>
@ -170,7 +170,7 @@
</ul></li> </ul></li>
</ul></div> </ul></div>
<div class="section level4"> <div class="section level4">
<h4 id="changed-2-1-1-9270">Changed<a class="anchor" aria-label="anchor" href="#changed-2-1-1-9270"></a></h4> <h4 id="changed-2-1-1-9272">Changed<a class="anchor" aria-label="anchor" href="#changed-2-1-1-9272"></a></h4>
<ul><li>SIR interpretation <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> <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> <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>
@ -234,6 +234,7 @@
<li>Fix for using a manual value for <code>mo_transform</code> in <code><a href="../reference/antibiogram.html">antibiogram()</a></code> <li>Fix for using a manual value for <code>mo_transform</code> in <code><a href="../reference/antibiogram.html">antibiogram()</a></code>
</li> </li>
<li>Fixed a bug for when <code><a href="../reference/antibiogram.html">antibiogram()</a></code> returns an empty data set</li> <li>Fixed a bug for when <code><a href="../reference/antibiogram.html">antibiogram()</a></code> returns an empty data set</li>
<li>Added Sensititre codes for animals, antimicrobials and microorganisms</li>
<li>Fix for mapping ‘high level’ antimicrobials in <code><a href="../reference/as.ab.html">as.ab()</a></code> (amphotericin B-high, gentamicin-high, kanamycin-high, streptomycin-high, tobramycin-high)</li> <li>Fix for mapping ‘high level’ antimicrobials in <code><a href="../reference/as.ab.html">as.ab()</a></code> (amphotericin B-high, gentamicin-high, kanamycin-high, streptomycin-high, tobramycin-high)</li>
<li>Improved overall algorithm of <code><a href="../reference/as.ab.html">as.ab()</a></code> for better performance and accuracy, including the new function <code>as_reset_session()</code> to remove earlier coercions.</li> <li>Improved overall algorithm of <code><a href="../reference/as.ab.html">as.ab()</a></code> for better performance and accuracy, including the new function <code>as_reset_session()</code> to remove earlier coercions.</li>
<li>Improved overall algorithm of <code><a href="../reference/as.mo.html">as.mo()</a></code> for better performance and accuracy, specifically: <li>Improved overall algorithm of <code><a href="../reference/as.mo.html">as.mo()</a></code> for better performance and accuracy, specifically:
@ -252,7 +253,7 @@
<li>Added console colours support of <code>sir</code> class for Positron</li> <li>Added console colours support of <code>sir</code> class for Positron</li>
</ul></div> </ul></div>
<div class="section level4"> <div class="section level4">
<h4 id="other-2-1-1-9270">Other<a class="anchor" aria-label="anchor" href="#other-2-1-1-9270"></a></h4> <h4 id="other-2-1-1-9272">Other<a class="anchor" aria-label="anchor" href="#other-2-1-1-9272"></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 will remain to work.</li> <ul><li>New website domain: <a href="https://amr-for-r.org" class="uri">https://amr-for-r.org</a>! The old domain 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 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> <li>Added Matthew Saab, Dr. Jordan Stull, and Prof. Javier Sanchez as contributors for their tremendous input on veterinary breakpoints and interpretations</li>
@ -263,7 +264,7 @@
</ul></div> </ul></div>
</div> </div>
<div class="section level3"> <div class="section level3">
<h3 id="older-versions-2-1-1-9270">Older Versions<a class="anchor" aria-label="anchor" href="#older-versions-2-1-1-9270"></a></h3> <h3 id="older-versions-2-1-1-9272">Older Versions<a class="anchor" aria-label="anchor" href="#older-versions-2-1-1-9272"></a></h3>
<p>This changelog only contains changes from AMR v3.0 (March 2025) and later.</p> <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> <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> <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
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@ -11,7 +11,7 @@ articles:
PCA: PCA.html PCA: PCA.html
WHONET: WHONET.html WHONET: WHONET.html
WISCA: WISCA.html WISCA: WISCA.html
last_built: 2025-05-04T12:29Z last_built: 2025-05-04T16:54Z
urls: urls:
reference: https://amr-for-r.org/reference reference: https://amr-for-r.org/reference
article: https://amr-for-r.org/articles article: https://amr-for-r.org/articles

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@ -7,7 +7,7 @@
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@ -7,7 +7,7 @@
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2
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@ -21,7 +21,7 @@ The AMR package is available in English, Arabic, Bengali, Chinese, Czech, Danish
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

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@ -7,7 +7,7 @@
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@ -7,7 +7,7 @@
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@ -7,7 +7,7 @@
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@ -7,7 +7,7 @@
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2
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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@ -7,7 +7,7 @@
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2
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@ -7,7 +7,7 @@
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@ -7,7 +7,7 @@
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2
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@ -9,7 +9,7 @@ Adhering to previously described approaches (see Source) and especially the Baye
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@ -17,7 +17,7 @@ my_data_with_all_these_columns %&amp;gt;%
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@ -7,7 +7,7 @@
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@ -146,11 +146,11 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> ACM 6<span style="text-decoration: underline;">450</span>012 Acety… Macr… <span style="color: #949494;">&lt;chr&gt;</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #949494;">&lt;chr [1]&gt;</span> <span style="color: #949494;">&lt;chr&gt;</span> </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> ACM 6<span style="text-decoration: underline;">450</span>012 Acety… Macr… <span style="color: #949494;">&lt;chr&gt;</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #949494;">&lt;chr [1]&gt;</span> <span style="color: #949494;">&lt;chr&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> ASP 49<span style="text-decoration: underline;">787</span>020 Acety… Macr… <span style="color: #949494;">&lt;chr&gt;</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #949494;">&lt;chr [1]&gt;</span> <span style="color: #949494;">&lt;chr&gt;</span> </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> ASP 49<span style="text-decoration: underline;">787</span>020 Acety… Macr… <span style="color: #949494;">&lt;chr&gt;</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #949494;">&lt;chr [1]&gt;</span> <span style="color: #949494;">&lt;chr&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> ALS <span style="text-decoration: underline;">8</span>954 Aldes… Othe… <span style="color: #949494;">&lt;chr&gt;</span> Drugs for… Drugs for… <span style="color: #949494;">&lt;chr [1]&gt;</span> <span style="color: #949494;">&lt;chr&gt;</span> </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> ALS <span style="text-decoration: underline;">8</span>954 Aldes… Othe… <span style="color: #949494;">&lt;chr&gt;</span> Drugs for… Drugs for… <span style="color: #949494;">&lt;chr [1]&gt;</span> <span style="color: #949494;">&lt;chr&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> AMK <span style="text-decoration: underline;">37</span>768 Amika… Amin… <span style="color: #949494;">&lt;chr&gt;</span> Aminoglyc… Other ami… <span style="color: #949494;">&lt;chr [5]&gt;</span> <span style="color: #949494;">&lt;chr&gt;</span> </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> AMK <span style="text-decoration: underline;">37</span>768 Amika… Amin… <span style="color: #949494;">&lt;chr&gt;</span> Aminoglyc… Other ami… <span style="color: #949494;">&lt;chr [6]&gt;</span> <span style="color: #949494;">&lt;chr&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> AKF <span style="color: #BB0000;">NA</span> Amika… Amin… <span style="color: #949494;">&lt;chr&gt;</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #949494;">&lt;chr [1]&gt;</span> <span style="color: #949494;">&lt;chr&gt;</span> </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> AKF <span style="color: #BB0000;">NA</span> Amika… Amin… <span style="color: #949494;">&lt;chr&gt;</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #949494;">&lt;chr [1]&gt;</span> <span style="color: #949494;">&lt;chr&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> AMO <span style="text-decoration: underline;">54</span>260 Amoro… Anti… <span style="color: #949494;">&lt;chr&gt;</span> Antifunga… Other ant… <span style="color: #949494;">&lt;chr [1]&gt;</span> <span style="color: #949494;">&lt;chr&gt;</span> </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> AMO <span style="text-decoration: underline;">54</span>260 Amoro… Anti… <span style="color: #949494;">&lt;chr&gt;</span> Antifunga… Other ant… <span style="color: #949494;">&lt;chr [1]&gt;</span> <span style="color: #949494;">&lt;chr&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> AMX <span style="text-decoration: underline;">33</span>613 Amoxi… Beta… <span style="color: #949494;">&lt;chr&gt;</span> Beta-lact… Penicilli… <span style="color: #949494;">&lt;chr [3]&gt;</span> <span style="color: #949494;">&lt;chr&gt;</span> </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> AMX <span style="text-decoration: underline;">33</span>613 Amoxi… Beta… <span style="color: #949494;">&lt;chr&gt;</span> Beta-lact… Penicilli… <span style="color: #949494;">&lt;chr [4]&gt;</span> <span style="color: #949494;">&lt;chr&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> AMC 23<span style="text-decoration: underline;">665</span>637 Amoxi… Beta… <span style="color: #949494;">&lt;chr&gt;</span> Beta-lact… Combinati… <span style="color: #949494;">&lt;chr [5]&gt;</span> <span style="color: #949494;">&lt;chr&gt;</span> </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> AMC 23<span style="text-decoration: underline;">665</span>637 Amoxi… Beta… <span style="color: #949494;">&lt;chr&gt;</span> Beta-lact… Combinati… <span style="color: #949494;">&lt;chr [6]&gt;</span> <span style="color: #949494;">&lt;chr&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> AXS <span style="text-decoration: underline;">465</span>441 Amoxi… Beta… <span style="color: #949494;">&lt;chr&gt;</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #949494;">&lt;chr [1]&gt;</span> <span style="color: #949494;">&lt;chr&gt;</span> </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> AXS <span style="text-decoration: underline;">465</span>441 Amoxi… Beta… <span style="color: #949494;">&lt;chr&gt;</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #949494;">&lt;chr [1]&gt;</span> <span style="color: #949494;">&lt;chr&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 487 more rows</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 487 more rows</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 5 more variables: oral_ddd &lt;dbl&gt;, oral_units &lt;chr&gt;, iv_ddd &lt;dbl&gt;,</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 5 more variables: oral_ddd &lt;dbl&gt;, oral_units &lt;chr&gt;, iv_ddd &lt;dbl&gt;,</span></span>

6
reference/as.ab.html
View File

@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</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="">2.1.1.9270</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9272</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -141,8 +141,10 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'ab'</span> <span class="r-out co"><span class="r-pr">#&gt;</span> Class 'ab'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] ERY</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] ERY</span>
<span class="r-in"><span><span class="fu">as.ab</span><span class="op">(</span><span class="st">"J 01 FA 01"</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="fu">as.ab</span><span class="op">(</span><span class="st">"J 01 FA 01"</span><span class="op">)</span></span></span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in <span style="background-color: #EEEEEE;">as.ab()</span>: these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "J 01 FA 01".</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'ab'</span> <span class="r-out co"><span class="r-pr">#&gt;</span> Class 'ab'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] ERY</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] &lt;NA&gt;</span>
<span class="r-in"><span><span class="fu">as.ab</span><span class="op">(</span><span class="st">"Erythromycin"</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="fu">as.ab</span><span class="op">(</span><span class="st">"Erythromycin"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'ab'</span> <span class="r-out co"><span class="r-pr">#&gt;</span> Class 'ab'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] ERY</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] ERY</span>

6
reference/as.av.html
View File

@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</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="">2.1.1.9270</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9272</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -133,8 +133,10 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'av'</span> <span class="r-out co"><span class="r-pr">#&gt;</span> Class 'av'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] ACI</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] ACI</span>
<span class="r-in"><span><span class="fu">as.av</span><span class="op">(</span><span class="st">"J 05 AB 01"</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="fu">as.av</span><span class="op">(</span><span class="st">"J 05 AB 01"</span><span class="op">)</span></span></span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in <span style="background-color: #EEEEEE;">as.av()</span>: these values could not be coerced to a valid antiviral drug</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "J 05 AB 01".</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'av'</span> <span class="r-out co"><span class="r-pr">#&gt;</span> Class 'av'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] ACI</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] &lt;NA&gt;</span>
<span class="r-in"><span><span class="fu">as.av</span><span class="op">(</span><span class="st">"Aciclovir"</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="fu">as.av</span><span class="op">(</span><span class="st">"Aciclovir"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'av'</span> <span class="r-out co"><span class="r-pr">#&gt;</span> Class 'av'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] ACI</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] ACI</span>

2
reference/as.disk.html
View File

@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</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="">2.1.1.9270</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9272</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"> <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> <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="">2.1.1.9270</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9272</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"> <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> <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="">2.1.1.9270</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9272</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

25
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> <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="">2.1.1.9270</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9272</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -80,8 +80,8 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
<span> <span class="cn">FALSE</span><span class="op">)</span>, include_screening <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_include_screening"</span>, <span class="cn">FALSE</span><span class="op">)</span>,</span> <span> <span class="cn">FALSE</span><span class="op">)</span>, include_screening <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_include_screening"</span>, <span class="cn">FALSE</span><span class="op">)</span>,</span>
<span> include_PKPD <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_include_PKPD"</span>, <span class="cn">TRUE</span><span class="op">)</span>,</span> <span> include_PKPD <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_include_PKPD"</span>, <span class="cn">TRUE</span><span class="op">)</span>,</span>
<span> breakpoint_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_breakpoint_type"</span>, <span class="st">"human"</span><span class="op">)</span>, host <span class="op">=</span> <span class="cn">NULL</span>,</span> <span> breakpoint_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_breakpoint_type"</span>, <span class="st">"human"</span><span class="op">)</span>, host <span class="op">=</span> <span class="cn">NULL</span>,</span>
<span> verbose <span class="op">=</span> <span class="cn">FALSE</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>, conserve_capped_values <span class="op">=</span> <span class="cn">NULL</span>,</span> <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>, verbose <span class="op">=</span> <span class="cn">FALSE</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>
<span> <span class="va">...</span><span class="op">)</span></span> <span> conserve_capped_values <span class="op">=</span> <span class="cn">NULL</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span> <span></span>
<span><span class="co"># S3 method for class 'disk'</span></span> <span><span class="co"># S3 method for class 'disk'</span></span>
<span><span class="fu">as.sir</span><span class="op">(</span><span class="va">x</span>, mo <span class="op">=</span> <span class="cn">NULL</span>, ab <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/deparse.html" class="external-link">deparse</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/substitute.html" class="external-link">substitute</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span><span class="op">)</span>,</span> <span><span class="fu">as.sir</span><span class="op">(</span><span class="va">x</span>, mo <span class="op">=</span> <span class="cn">NULL</span>, ab <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/deparse.html" class="external-link">deparse</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/substitute.html" class="external-link">substitute</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span><span class="op">)</span>,</span>
@ -92,7 +92,8 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
<span> <span class="cn">FALSE</span><span class="op">)</span>, include_screening <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_include_screening"</span>, <span class="cn">FALSE</span><span class="op">)</span>,</span> <span> <span class="cn">FALSE</span><span class="op">)</span>, include_screening <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_include_screening"</span>, <span class="cn">FALSE</span><span class="op">)</span>,</span>
<span> include_PKPD <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_include_PKPD"</span>, <span class="cn">TRUE</span><span class="op">)</span>,</span> <span> include_PKPD <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_include_PKPD"</span>, <span class="cn">TRUE</span><span class="op">)</span>,</span>
<span> breakpoint_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_breakpoint_type"</span>, <span class="st">"human"</span><span class="op">)</span>, host <span class="op">=</span> <span class="cn">NULL</span>,</span> <span> breakpoint_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_breakpoint_type"</span>, <span class="st">"human"</span><span class="op">)</span>, host <span class="op">=</span> <span class="cn">NULL</span>,</span>
<span> verbose <span class="op">=</span> <span class="cn">FALSE</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> 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>, verbose <span class="op">=</span> <span class="cn">FALSE</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>
<span> <span class="va">...</span><span class="op">)</span></span>
<span></span> <span></span>
<span><span class="co"># S3 method for class 'data.frame'</span></span> <span><span class="co"># S3 method for class 'data.frame'</span></span>
<span><span class="fu">as.sir</span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span>, col_mo <span class="op">=</span> <span class="cn">NULL</span>,</span> <span><span class="fu">as.sir</span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span>, col_mo <span class="op">=</span> <span class="cn">NULL</span>,</span>
@ -104,8 +105,8 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
<span> <span class="cn">FALSE</span><span class="op">)</span>, include_screening <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_include_screening"</span>, <span class="cn">FALSE</span><span class="op">)</span>,</span> <span> <span class="cn">FALSE</span><span class="op">)</span>, include_screening <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_include_screening"</span>, <span class="cn">FALSE</span><span class="op">)</span>,</span>
<span> include_PKPD <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_include_PKPD"</span>, <span class="cn">TRUE</span><span class="op">)</span>,</span> <span> include_PKPD <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_include_PKPD"</span>, <span class="cn">TRUE</span><span class="op">)</span>,</span>
<span> breakpoint_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_breakpoint_type"</span>, <span class="st">"human"</span><span class="op">)</span>, host <span class="op">=</span> <span class="cn">NULL</span>,</span> <span> breakpoint_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_breakpoint_type"</span>, <span class="st">"human"</span><span class="op">)</span>, host <span class="op">=</span> <span class="cn">NULL</span>,</span>
<span> verbose <span class="op">=</span> <span class="cn">FALSE</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>, parallel <span class="op">=</span> <span class="cn">FALSE</span>,</span> <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>, verbose <span class="op">=</span> <span class="cn">FALSE</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>
<span> max_cores <span class="op">=</span> <span class="op">-</span><span class="fl">1</span>, conserve_capped_values <span class="op">=</span> <span class="cn">NULL</span><span class="op">)</span></span> <span> parallel <span class="op">=</span> <span class="cn">FALSE</span>, max_cores <span class="op">=</span> <span class="op">-</span><span class="fl">1</span>, conserve_capped_values <span class="op">=</span> <span class="cn">NULL</span><span class="op">)</span></span>
<span></span> <span></span>
<span><span class="fu">sir_interpretation_history</span><span class="op">(</span>clean <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div> <span><span class="fu">sir_interpretation_history</span><span class="op">(</span>clean <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div>
</div> </div>
@ -199,6 +200,10 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
<dd><p>A vector (or column name) with <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a>s to indicate the host. Only useful for veterinary breakpoints, as it requires <code>breakpoint_type = "animal"</code>. The values can be any text resembling the animal species, even in any of the 28 supported languages of this package. For foreign languages, be sure to set the language with <code><a href="translate.html">set_AMR_locale()</a></code> (though it will be automatically guessed based on the system language).</p></dd> <dd><p>A vector (or column name) with <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a>s to indicate the host. Only useful for veterinary breakpoints, as it requires <code>breakpoint_type = "animal"</code>. The values can be any text resembling the animal species, even in any of the 28 supported languages of this package. For foreign languages, be sure to set the language with <code><a href="translate.html">set_AMR_locale()</a></code> (though it will be automatically guessed based on the system language).</p></dd>
<dt id="arg-language">language<a class="anchor" aria-label="anchor" href="#arg-language"></a></dt>
<dd><p>Language to convert values set in <code>host</code> when using animal breakpoints. Use one of these supported language names or <a href="https://en.wikipedia.org/wiki/ISO_639-1" class="external-link">ISO 639-1 codes</a>: English (en), Arabic (ar), Bengali (bn), Chinese (zh), Czech (cs), Danish (da), Dutch (nl), Finnish (fi), French (fr), German (de), Greek (el), Hindi (hi), Indonesian (id), Italian (it), Japanese (ja), Korean (ko), Norwegian (no), Polish (pl), Portuguese (pt), Romanian (ro), Russian (ru), Spanish (es), Swahili (sw), Swedish (sv), Turkish (tr), Ukrainian (uk), Urdu (ur), or Vietnamese (vi).</p></dd>
<dt id="arg-verbose">verbose<a class="anchor" aria-label="anchor" href="#arg-verbose"></a></dt> <dt id="arg-verbose">verbose<a class="anchor" aria-label="anchor" href="#arg-verbose"></a></dt>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate that all notes should be printed during interpretation of MIC values or disk diffusion values.</p></dd> <dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate that all notes should be printed during interpretation of MIC values or disk diffusion values.</p></dd>
@ -409,10 +414,10 @@ 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> <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> 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: #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> 2025-05-04 <span style="color: #949494;">12:30:36</span> 1 MIC amoxicillin Escherich… human 8 </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2025-05-04 <span style="color: #949494;">16:54:58</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> 2025-05-04 <span style="color: #949494;">12:30:36</span> 1 MIC cipro Escherich… human 0.256 </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> 2025-05-04 <span style="color: #949494;">16:54:59</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> 2025-05-04 <span style="color: #949494;">12:30:36</span> 1 DISK tobra Escherich… human 16 </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> 2025-05-04 <span style="color: #949494;">16:54:59</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> 2025-05-04 <span style="color: #949494;">12:30:36</span> 1 DISK genta Escherich… human 18 </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> 2025-05-04 <span style="color: #949494;">16:54:59</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;"># 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;"># 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> <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
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</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="">2.1.1.9270</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9272</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"> <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
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</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="">2.1.1.9270</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9272</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"> <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
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</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="">2.1.1.9270</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9272</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"> <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
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</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="">2.1.1.9270</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9272</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"> <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
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</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="">2.1.1.9270</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9272</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"> <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
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@ -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> <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="">2.1.1.9270</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9272</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"> <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
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@ -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> <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="">2.1.1.9270</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9272</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"> <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
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</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="">2.1.1.9270</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9272</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"> <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
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</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="">2.1.1.9270</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9272</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"> <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
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@ -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> <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="">2.1.1.9270</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9272</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"> <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
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</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="">2.1.1.9270</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9272</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"> <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
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</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="">2.1.1.9270</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9272</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"> <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
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</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="">2.1.1.9270</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9272</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"> <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
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@ -9,7 +9,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</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="">2.1.1.9270</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9272</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"> <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
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</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="">2.1.1.9270</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9272</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"> <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
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@ -7,7 +7,7 @@
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<code><a href="microorganisms.codes.html">microorganisms.codes</a></code> <code><a href="microorganisms.codes.html">microorganisms.codes</a></code>
</dt> </dt>
<dd>Data Set with 5 063 Common Microorganism Codes</dd> <dd>Data Set with 6 036 Common Microorganism Codes</dd>
</dl><dl><dt> </dl><dl><dt>
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<!DOCTYPE html> <!DOCTYPE html>
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</nav><div class="container template-reference-topic"> </nav><div class="container template-reference-topic">
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<img src="../logo.svg" class="logo" alt=""><h1>Data Set with 5 063 Common Microorganism Codes</h1> <img src="../logo.svg" class="logo" alt=""><h1>Data Set with 6 036 Common Microorganism Codes</h1>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/R/data.R" class="external-link"><code>R/data.R</code></a></small> <small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/R/data.R" class="external-link"><code>R/data.R</code></a></small>
<div class="d-none name"><code>microorganisms.codes.Rd</code></div> <div class="d-none name"><code>microorganisms.codes.Rd</code></div>
</div> </div>
@ -60,7 +60,7 @@
<div class="section level2"> <div class="section level2">
<h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2> <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 5 063 observations and 2 variables:</p><ul><li><p><code>code</code><br> Commonly used code of a microorganism. <em><strong>This is a unique identifier.</strong></em></p></li> <p>A <a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble</a> with 6 036 observations and 2 variables:</p><ul><li><p><code>code</code><br> Commonly used code of a microorganism. <em><strong>This is a unique identifier.</strong></em></p></li>
<li><p><code>mo</code><br> ID of the microorganism in the <a href="microorganisms.html">microorganisms</a> data set</p></li> <li><p><code>mo</code><br> ID of the microorganism in the <a href="microorganisms.html">microorganisms</a> data set</p></li>
</ul></div> </ul></div>
<div class="section level2"> <div class="section level2">
@ -79,7 +79,7 @@
<div class="section level2"> <div class="section level2">
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> <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">microorganisms.codes</span></span></span> <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">microorganisms.codes</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 5,063 × 2</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 6,036 × 2</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> code mo </span> <span class="r-out co"><span class="r-pr">#&gt;</span> code mo </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;mo&gt;</span> </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;mo&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 1011 <span style="color: #949494;">B_</span>GRAMP </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 1011 <span style="color: #949494;">B_</span>GRAMP </span>
@ -92,7 +92,7 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 1100 <span style="color: #949494;">B_</span>STRPT </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 1100 <span style="color: #949494;">B_</span>STRPT </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 1101 <span style="color: #949494;">B_</span>STRPT<span style="color: #949494;">_</span>VIRI </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 1101 <span style="color: #949494;">B_</span>STRPT<span style="color: #949494;">_</span>VIRI </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 1102 <span style="color: #949494;">B_</span>STRPT<span style="color: #949494;">_</span>HAEM </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 1102 <span style="color: #949494;">B_</span>STRPT<span style="color: #949494;">_</span>HAEM </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 5,053 more rows</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 6,026 more rows</span></span>
<span class="r-in"><span></span></span> <span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># 'ECO' or 'eco' is the WHONET code for E. coli:</span></span></span> <span class="r-in"><span><span class="co"># 'ECO' or 'eco' is the WHONET code for E. coli:</span></span></span>
<span class="r-in"><span><span class="va">microorganisms.codes</span><span class="op">[</span><span class="va">microorganisms.codes</span><span class="op">$</span><span class="va">code</span> <span class="op">==</span> <span class="st">"ECO"</span>, <span class="op">]</span></span></span> <span class="r-in"><span><span class="va">microorganisms.codes</span><span class="op">[</span><span class="va">microorganisms.codes</span><span class="op">$</span><span class="va">code</span> <span class="op">==</span> <span class="st">"ECO"</span>, <span class="op">]</span></span></span>

2
reference/microorganisms.groups.html
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</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="">2.1.1.9270</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9272</small>
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2
reference/microorganisms.html
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@ -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> <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="">2.1.1.9270</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9272</small>
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2
reference/mo_matching_score.html
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</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="">2.1.1.9270</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9272</small>
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2
reference/mo_property.html
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</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="">2.1.1.9270</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9272</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"> <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
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@ -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> <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="">2.1.1.9270</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9272</small>
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2
reference/pca.html
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</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="">2.1.1.9270</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9272</small>
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2
reference/plot.html
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@ -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> <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="">2.1.1.9270</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9272</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"> <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
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@ -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> <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="">2.1.1.9270</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9272</small>
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2
reference/random.html
View File

@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</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="">2.1.1.9270</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9272</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"> <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> <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="">2.1.1.9270</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9272</small>
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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> <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="">2.1.1.9270</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9272</small>
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2
reference/top_n_microorganisms.html
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</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="">2.1.1.9270</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9272</small>
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2
reference/translate.html
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</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="">2.1.1.9270</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9272</small>
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2
search.json
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