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(v1.8.1) prerelease 1.8.1

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dr. M.S. (Matthijs) Berends
2022-03-14 16:36:10 +01:00
parent 08d387b5ce
commit 1b0983e382
98 changed files with 2958 additions and 1291 deletions
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8
docs/reference/AMR-deprecated.html
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@ -17,7 +17,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9004</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
</span>
</div>
@ -184,11 +184,13 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>retired</
<footer><div class="copyright">
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
Erwin E. A. Hassing.</p>
</div>
<div class="pkgdown">
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
2.0.2.</p>
</div>
</footer></div>

9
docs/reference/AMR.html
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@ -17,7 +17,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
</span>
</div>
@ -161,7 +161,6 @@
<p>Welcome to the <code>AMR</code> package.</p>
</div>
<div id="ref-usage">Usage,NULL</div>
<div id="details">
<h2>Details</h2>
@ -222,11 +221,13 @@ The Netherlands
<footer><div class="copyright">
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
Erwin E. A. Hassing.</p>
</div>
<div class="pkgdown">
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.0.</p>
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
2.0.2.</p>
</div>
</footer></div>

8
docs/reference/WHOCC.html
View File

@ -17,7 +17,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9004</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
</span>
</div>
@ -195,11 +195,13 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
<footer><div class="copyright">
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
Erwin E. A. Hassing.</p>
</div>
<div class="pkgdown">
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
2.0.2.</p>
</div>
</footer></div>

12
docs/reference/WHONET.html
View File

@ -17,7 +17,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
</span>
</div>
@ -161,7 +161,9 @@
<p>This example data set has the exact same structure as an export file from WHONET. Such files can be used with this package, as this example data set shows. The antibiotic results are from our <a href="example_isolates.html">example_isolates</a> data set. All patient names are created using online surname generators and are only in place for practice purposes.</p>
</div>
<div id="ref-usage">Usage,<div class="sourceCode"><pre class="sourceCode r"><code><span class="va">WHONET</span></code></pre></div></div>
<div id="ref-usage">
<div class="sourceCode"><pre class="sourceCode r"><code><span class="va">WHONET</span></code></pre></div>
</div>
<div id="format">
<h2>Format</h2>
@ -213,11 +215,13 @@
<footer><div class="copyright">
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
Erwin E. A. Hassing.</p>
</div>
<div class="pkgdown">
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.0.</p>
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
2.0.2.</p>
</div>
</footer></div>

2
docs/reference/ab_from_text.html
View File

@ -17,7 +17,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
</span>
</div>

2
docs/reference/ab_property.html
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@ -17,7 +17,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
</span>
</div>

2
docs/reference/age.html
View File

@ -17,7 +17,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
</span>
</div>

2
docs/reference/age_groups.html
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@ -17,7 +17,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
</span>
</div>

2
docs/reference/antibiotic_class_selectors.html
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@ -17,7 +17,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
</span>
</div>

8
docs/reference/antibiotics.html
View File

@ -17,7 +17,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9004</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
</span>
</div>
@ -259,11 +259,13 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
<footer><div class="copyright">
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
Erwin E. A. Hassing.</p>
</div>
<div class="pkgdown">
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
2.0.2.</p>
</div>
</footer></div>

2
docs/reference/as.ab.html
View File

@ -17,7 +17,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
</span>
</div>

2
docs/reference/as.disk.html
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@ -17,7 +17,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
</span>
</div>

2
docs/reference/as.mic.html
View File

@ -17,7 +17,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
</span>
</div>

2
docs/reference/as.mo.html
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@ -17,7 +17,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
</span>
</div>

2
docs/reference/as.rsi.html
View File

@ -17,7 +17,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
</span>
</div>

2
docs/reference/atc_online.html
View File

@ -17,7 +17,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
</span>
</div>

2
docs/reference/availability.html
View File

@ -17,7 +17,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
</span>
</div>

2
docs/reference/bug_drug_combinations.html
View File

@ -17,7 +17,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
</span>
</div>

8
docs/reference/catalogue_of_life.html
View File

@ -17,7 +17,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9004</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
</span>
</div>
@ -235,11 +235,13 @@ Function <code><a href="as.mo.html">as.mo()</a></code> to use the data for intel
<footer><div class="copyright">
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
Erwin E. A. Hassing.</p>
</div>
<div class="pkgdown">
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
2.0.2.</p>
</div>
</footer></div>

8
docs/reference/catalogue_of_life_version.html
View File

@ -17,7 +17,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9004</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
</span>
</div>
@ -200,11 +200,13 @@ This package contains the complete taxonomic tree of almost all microorganisms (
<footer><div class="copyright">
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
Erwin E. A. Hassing.</p>
</div>
<div class="pkgdown">
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
2.0.2.</p>
</div>
</footer></div>

2
docs/reference/count.html
View File

@ -18,7 +18,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
</span>
</div>

2
docs/reference/custom_eucast_rules.html
View File

@ -17,7 +17,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
</span>
</div>

12
docs/reference/dosage.html
View File

@ -17,7 +17,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
</span>
</div>
@ -161,7 +161,9 @@
<p>EUCAST breakpoints used in this package are based on the dosages in this data set. They can be retrieved with <code><a href="eucast_rules.html">eucast_dosage()</a></code>.</p>
</div>
<div id="ref-usage">Usage,<div class="sourceCode"><pre class="sourceCode r"><code><span class="va">dosage</span></code></pre></div></div>
<div id="ref-usage">
<div class="sourceCode"><pre class="sourceCode r"><code><span class="va">dosage</span></code></pre></div>
</div>
<div id="format">
<h2>Format</h2>
@ -200,11 +202,13 @@
<footer><div class="copyright">
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
Erwin E. A. Hassing.</p>
</div>
<div class="pkgdown">
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.0.</p>
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
2.0.2.</p>
</div>
</footer></div>

2
docs/reference/eucast_rules.html
View File

@ -18,7 +18,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
</span>
</div>

12
docs/reference/example_isolates.html
View File

@ -17,7 +17,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
</span>
</div>
@ -161,7 +161,9 @@
<p>A data set containing 2,000 microbial isolates with their full antibiograms. The data set reflects reality and can be used to practice AMR data analysis. For examples, please read <a href="https://msberends.github.io/AMR/articles/AMR.html">the tutorial on our website</a>.</p>
</div>
<div id="ref-usage">Usage,<div class="sourceCode"><pre class="sourceCode r"><code><span class="va">example_isolates</span></code></pre></div></div>
<div id="ref-usage">
<div class="sourceCode"><pre class="sourceCode r"><code><span class="va">example_isolates</span></code></pre></div>
</div>
<div id="format">
<h2>Format</h2>
@ -197,11 +199,13 @@
<footer><div class="copyright">
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
Erwin E. A. Hassing.</p>
</div>
<div class="pkgdown">
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.0.</p>
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
2.0.2.</p>
</div>
</footer></div>

12
docs/reference/example_isolates_unclean.html
View File

@ -17,7 +17,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
</span>
</div>
@ -161,7 +161,9 @@
<p>A data set containing 3,000 microbial isolates that are not cleaned up and consequently not ready for AMR data analysis. This data set can be used for practice.</p>
</div>
<div id="ref-usage">Usage,<div class="sourceCode"><pre class="sourceCode r"><code><span class="va">example_isolates_unclean</span></code></pre></div></div>
<div id="ref-usage">
<div class="sourceCode"><pre class="sourceCode r"><code><span class="va">example_isolates_unclean</span></code></pre></div>
</div>
<div id="format">
<h2>Format</h2>
@ -192,11 +194,13 @@
<footer><div class="copyright">
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
Erwin E. A. Hassing.</p>
</div>
<div class="pkgdown">
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.0.</p>
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
2.0.2.</p>
</div>
</footer></div>

2
docs/reference/first_isolate.html
View File

@ -18,7 +18,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
</span>
</div>

8
docs/reference/g.test.html
View File

@ -17,7 +17,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9004</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
</span>
</div>
@ -323,11 +323,13 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>questioni
<footer><div class="copyright">
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
Erwin E. A. Hassing.</p>
</div>
<div class="pkgdown">
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
2.0.2.</p>
</div>
</footer></div>

2
docs/reference/get_episode.html
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@ -17,7 +17,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
</span>
</div>

2
docs/reference/ggplot_pca.html
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@ -17,7 +17,7 @@
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
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</span>
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2
docs/reference/ggplot_rsi.html
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@ -17,7 +17,7 @@
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<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
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</span>
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2
docs/reference/guess_ab_col.html
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@ -17,7 +17,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
</span>
</div>

2
docs/reference/index.html
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@ -17,7 +17,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
</span>
</div>

12
docs/reference/intrinsic_resistant.html
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@ -17,7 +17,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
</span>
</div>
@ -161,7 +161,9 @@
<p>Data set containing defined intrinsic resistance by EUCAST of all bug-drug combinations.</p>
</div>
<div id="ref-usage">Usage,<div class="sourceCode"><pre class="sourceCode r"><code><span class="va">intrinsic_resistant</span></code></pre></div></div>
<div id="ref-usage">
<div class="sourceCode"><pre class="sourceCode r"><code><span class="va">intrinsic_resistant</span></code></pre></div>
</div>
<div id="format">
<h2>Format</h2>
@ -208,11 +210,13 @@
<footer><div class="copyright">
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
Erwin E. A. Hassing.</p>
</div>
<div class="pkgdown">
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.0.</p>
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2
docs/reference/italicise_taxonomy.html
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@ -17,7 +17,7 @@
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<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
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</span>
</div>

2
docs/reference/join.html
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@ -17,7 +17,7 @@
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<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
</span>
</div>

2
docs/reference/key_antimicrobials.html
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@ -17,7 +17,7 @@
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</span>
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2
docs/reference/kurtosis.html
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@ -17,7 +17,7 @@
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<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
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</span>
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2
docs/reference/lifecycle.html
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@ -19,7 +19,7 @@ This page contains a section for every lifecycle (with text borrowed from the af
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</span>
</div>

2
docs/reference/like.html
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@ -17,7 +17,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
</span>
</div>

2
docs/reference/mdro.html
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@ -17,7 +17,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
</span>
</div>

8
docs/reference/microorganisms.codes.html
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@ -17,7 +17,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9004</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
</span>
</div>
@ -203,11 +203,13 @@ This package contains the complete taxonomic tree of almost all microorganisms (
<footer><div class="copyright">
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
Erwin E. A. Hassing.</p>
</div>
<div class="pkgdown">
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
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docs/reference/microorganisms.html
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@ -17,7 +17,7 @@
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<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9004</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
</span>
</div>
@ -254,11 +254,13 @@ This package contains the complete taxonomic tree of almost all microorganisms (
<footer><div class="copyright">
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
Erwin E. A. Hassing.</p>
</div>
<div class="pkgdown">
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
2.0.2.</p>
</div>
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8
docs/reference/microorganisms.old.html
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@ -17,7 +17,7 @@
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9004</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
</span>
</div>
@ -210,11 +210,13 @@ This package contains the complete taxonomic tree of almost all microorganisms (
<footer><div class="copyright">
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
Erwin E. A. Hassing.</p>
</div>
<div class="pkgdown">
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
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2
docs/reference/mo_matching_score.html
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@ -17,7 +17,7 @@
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</span>
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2
docs/reference/mo_property.html
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@ -17,7 +17,7 @@
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</span>
</div>

2
docs/reference/mo_source.html
View File

@ -18,7 +18,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
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</span>
</div>

2
docs/reference/pca.html
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@ -17,7 +17,7 @@
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
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</span>
</div>

2
docs/reference/plot.html
View File

@ -17,7 +17,7 @@
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
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</span>
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2
docs/reference/proportion.html
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@ -18,7 +18,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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</span>
</div>

2
docs/reference/random.html
View File

@ -17,7 +17,7 @@
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<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
</span>
</div>

2
docs/reference/resistance_predict.html
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@ -17,7 +17,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
</span>
</div>

12
docs/reference/rsi_translation.html
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@ -17,7 +17,7 @@
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<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
</span>
</div>
@ -161,7 +161,9 @@
<p>Data set containing reference data to interpret MIC and disk diffusion to R/SI values, according to international guidelines. Currently implemented guidelines are EUCAST (2011-2021) and CLSI (2010-2021). Use <code><a href="as.rsi.html">as.rsi()</a></code> to transform MICs or disks measurements to R/SI values.</p>
</div>
<div id="ref-usage">Usage,<div class="sourceCode"><pre class="sourceCode r"><code><span class="va">rsi_translation</span></code></pre></div></div>
<div id="ref-usage">
<div class="sourceCode"><pre class="sourceCode r"><code><span class="va">rsi_translation</span></code></pre></div>
</div>
<div id="format">
<h2>Format</h2>
@ -206,11 +208,13 @@
<footer><div class="copyright">
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
Erwin E. A. Hassing.</p>
</div>
<div class="pkgdown">
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.0.</p>
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
2.0.2.</p>
</div>
</footer></div>

2
docs/reference/skewness.html
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@ -18,7 +18,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
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<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
</span>
</div>

2
docs/reference/translate.html
View File

@ -17,7 +17,7 @@
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<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
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</span>
</div>