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(v1.7.1.9054) mdro() update - fixes #49, first_isolate() speedup

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dr. M.S. (Matthijs) Berends
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@ -58,8 +58,6 @@
<!-- mathjax -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
@ -71,15 +69,9 @@
</head>
<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
@ -93,7 +85,7 @@
</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="Latest development version">1.7.1.9030</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9054</span>
</span>
</div>
@ -238,7 +230,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>Transform Input to Disk Diffusion Diameters</h1>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/main/R/disk.R'><code>R/disk.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/disk.R'><code>R/disk.R</code></a></small>
<div class="hidden name"><code>as.disk.Rd</code></div>
</div>
@ -246,9 +238,11 @@
<p>This transforms a vector to a new class <code>disk</code>, which is a disk diffusion growth zone size (around an antibiotic disk) in millimetres between 6 and 50.</p>
</div>
<div class="ref-usage sourceCode"><pre class='sourceCode r'><code><span class='fu'>as.disk</span><span class='op'>(</span><span class='va'>x</span>, na.rm <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
<pre class="usage"><span class='fu'>as.disk</span><span class='op'>(</span><span class='va'>x</span>, na.rm <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
<span class='fu'>is.disk</span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span></code></pre></div>
<span class='va'>NA_disk_</span>
<span class='fu'>is.disk</span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span></pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@ -263,12 +257,16 @@
</tr>
</table>
<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
<p>An object of class <code>disk</code> (inherits from <code>integer</code>) of length 1.</p>
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>An <a href='https://rdrr.io/r/base/integer.html'>integer</a> with additional class <code>disk</code></p>
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>Interpret disk values as RSI values with <code><a href='as.rsi.html'>as.rsi()</a></code>. It supports guidelines from EUCAST and CLSI.</p>
<p><code>NA_disk_</code> is a missing value of the new <code>&lt;disk&gt;</code> class.</p>
<h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable Lifecycle</h2>
@ -286,7 +284,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<div class='dont-index'><p><code><a href='as.rsi.html'>as.rsi()</a></code></p></div>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<div class="ref-examples sourceCode"><pre class='sourceCode r'><code><span class='co'># \donttest{</span>
<pre class="examples"><span class='co'># \donttest{</span>
<span class='co'># transform existing disk zones to the `disk` class</span>
<span class='va'>df</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span><span class='op'>(</span>microorganism <span class='op'>=</span> <span class='st'>"E. coli"</span>,
AMP <span class='op'>=</span> <span class='fl'>20</span>,
@ -305,7 +303,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<span class='fu'><a href='as.rsi.html'>as.rsi</a></span><span class='op'>(</span><span class='va'>df</span><span class='op'>)</span>
<span class='co'># }</span>
</code></pre></div>
</pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<nav id="toc" data-toggle="toc" class="sticky-top">
@ -317,11 +315,11 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<footer>
<div class="copyright">
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
</div>
<div class="pkgdown">
<p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 1.6.1.9001.</p></p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
</div>
</footer>
@ -330,8 +328,6 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
</body>
</html>

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</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="Latest development version">1.7.1.9053</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9054</span>
</span>
</div>
@ -240,6 +240,8 @@
<pre class="usage"><span class='fu'>as.rsi</span><span class='op'>(</span><span class='va'>x</span>, <span class='va'>...</span><span class='op'>)</span>
<span class='va'>NA_rsi_</span>
<span class='fu'>is.rsi</span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span>
<span class='fu'>is.rsi.eligible</span><span class='op'>(</span><span class='va'>x</span>, threshold <span class='op'>=</span> <span class='fl'>0.05</span><span class='op'>)</span>
@ -330,6 +332,9 @@
</tr>
</table>
<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
<p>An object of class <code>rsi</code> (inherits from <code>ordered</code>, <code>factor</code>) of length 1.</p>
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>Ordered <a href='https://rdrr.io/r/base/factor.html'>factor</a> with new class <code>&lt;rsi&gt;</code></p>
@ -378,6 +383,7 @@
<p>The function <code>is.rsi()</code> detects if the input contains class <code>&lt;rsi&gt;</code>. If the input is a <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a>, it iterates over all columns and returns a <a href='https://rdrr.io/r/base/logical.html'>logical</a> vector.</p>
<p>The function <code>is.rsi.eligible()</code> returns <code>TRUE</code> when a columns contains at most 5% invalid antimicrobial interpretations (not S and/or I and/or R), and <code>FALSE</code> otherwise. The threshold of 5% can be set with the <code>threshold</code> argument. If the input is a <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a>, it iterates over all columns and returns a <a href='https://rdrr.io/r/base/logical.html'>logical</a> vector.</p>
<p><code>NA_rsi_</code> is a missing value of the new <code>&lt;rsi&gt;</code> class.</p>
<h2 class="hasAnchor" id="interpretation-of-r-and-s-i"><a class="anchor" href="#interpretation-of-r-and-s-i"></a>Interpretation of R and S/I</h2>
@ -509,7 +515,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<footer>
<div class="copyright">
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, Dennis Souverein, Erwin E. A. Hassing, Christian F. Luz.</p>
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
</div>
<div class="pkgdown">

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@ -58,8 +58,6 @@
<!-- mathjax -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
@ -71,15 +69,9 @@
</head>
<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
@ -93,7 +85,7 @@
</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="Latest development version">1.7.1.9040</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9054</span>
</span>
</div>
@ -238,7 +230,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>Define Custom EUCAST Rules</h1>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/main/R/custom_eucast_rules.R'><code>R/custom_eucast_rules.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/custom_eucast_rules.R'><code>R/custom_eucast_rules.R</code></a></small>
<div class="hidden name"><code>custom_eucast_rules.Rd</code></div>
</div>
@ -246,7 +238,7 @@
<p>Define custom EUCAST rules for your organisation or specific analysis and use the output of this function in <code><a href='eucast_rules.html'>eucast_rules()</a></code>.</p>
</div>
<div class="ref-usage sourceCode"><pre class='sourceCode r'><code><span class='fu'>custom_eucast_rules</span><span class='op'>(</span><span class='va'>...</span><span class='op'>)</span></code></pre></div>
<pre class="usage"><span class='fu'>custom_eucast_rules</span><span class='op'>(</span><span class='va'>...</span><span class='op'>)</span></pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@ -267,14 +259,14 @@
<h3 class='hasAnchor' id='basics'><a class='anchor' aria-hidden='true' href='#basics'></a>Basics</h3>
<h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Basics</h3>
<p>If you are familiar with the <code><a href='https://dplyr.tidyverse.org/reference/case_when.html'>case_when()</a></code> function of the <code>dplyr</code> package, you will recognise the input method to set your own rules. Rules must be set using what <span style="R">R</span> considers to be the 'formula notation'. The rule itself is written <em>before</em> the tilde (<code><a href='https://rdrr.io/r/base/tilde.html'>~</a></code>) and the consequence of the rule is written <em>after</em> the tilde:</p><pre class='sourceCode r'><code><span class='va'>x</span> <span class='op'>&lt;-</span> <span class='fu'>custom_eucast_rules</span><span class='op'>(</span><span class='va'>TZP</span> <span class='op'>==</span> <span class='st'>"S"</span> <span class='op'>~</span> <span class='va'>aminopenicillins</span> <span class='op'>==</span> <span class='st'>"S"</span>,
<p>If you are familiar with the <code><a href='https://dplyr.tidyverse.org/reference/case_when.html'>case_when()</a></code> function of the <code>dplyr</code> package, you will recognise the input method to set your own rules. Rules must be set using what <span style="R">R</span> considers to be the 'formula notation'. The rule itself is written <em>before</em> the tilde (<code><a href='https://rdrr.io/r/base/tilde.html'>~</a></code>) and the consequence of the rule is written <em>after</em> the tilde:</p><pre><span class='va'>x</span> <span class='op'>&lt;-</span> <span class='fu'>custom_eucast_rules</span><span class='op'>(</span><span class='va'>TZP</span> <span class='op'>==</span> <span class='st'>"S"</span> <span class='op'>~</span> <span class='va'>aminopenicillins</span> <span class='op'>==</span> <span class='st'>"S"</span>,
<span class='va'>TZP</span> <span class='op'>==</span> <span class='st'>"R"</span> <span class='op'>~</span> <span class='va'>aminopenicillins</span> <span class='op'>==</span> <span class='st'>"R"</span><span class='op'>)</span>
</code></pre>
</pre>
<p>These are two custom EUCAST rules: if TZP (piperacillin/tazobactam) is "S", all aminopenicillins (ampicillin and amoxicillin) must be made "S", and if TZP is "R", aminopenicillins must be made "R". These rules can also be printed to the console, so it is immediately clear how they work:</p><pre class='sourceCode r'><code><span class='va'>x</span>
<p>These are two custom EUCAST rules: if TZP (piperacillin/tazobactam) is "S", all aminopenicillins (ampicillin and amoxicillin) must be made "S", and if TZP is "R", aminopenicillins must be made "R". These rules can also be printed to the console, so it is immediately clear how they work:</p><pre><span class='va'>x</span>
<span class='co'>#&gt; A set of custom EUCAST rules:</span>
<span class='co'>#&gt; </span>
<span class='co'>#&gt; 1. If TZP is S then set to S:</span>
@ -282,9 +274,9 @@
<span class='co'>#&gt; </span>
<span class='co'>#&gt; 2. If TZP is R then set to R:</span>
<span class='co'>#&gt; amoxicillin (AMX), ampicillin (AMP)</span>
</code></pre>
</pre>
<p>The rules (the part <em>before</em> the tilde, in above example <code>TZP == "S"</code> and <code>TZP == "R"</code>) must be evaluable in your data set: it should be able to run as a filter in your data set without errors. This means for the above example that the column <code>TZP</code> must exist. We will create a sample data set and test the rules set:</p><pre class='sourceCode r'><code><span class='va'>df</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span><span class='op'>(</span>mo <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"E. coli"</span>, <span class='st'>"K. pneumoniae"</span><span class='op'>)</span>,
<p>The rules (the part <em>before</em> the tilde, in above example <code>TZP == "S"</code> and <code>TZP == "R"</code>) must be evaluable in your data set: it should be able to run as a filter in your data set without errors. This means for the above example that the column <code>TZP</code> must exist. We will create a sample data set and test the rules set:</p><pre><span class='va'>df</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span><span class='op'>(</span>mo <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"E. coli"</span>, <span class='st'>"K. pneumoniae"</span><span class='op'>)</span>,
TZP <span class='op'>=</span> <span class='st'>"R"</span>,
amox <span class='op'>=</span> <span class='st'>""</span>,
AMP <span class='op'>=</span> <span class='st'>""</span><span class='op'>)</span>
@ -297,23 +289,23 @@
<span class='co'>#&gt; mo TZP amox AMP</span>
<span class='co'>#&gt; 1 E. coli R R R </span>
<span class='co'>#&gt; 2 K. pneumoniae R R R </span>
</code></pre>
</pre>
<h3 class='hasAnchor' id='using-taxonomic-properties-in-rules'><a class='anchor' aria-hidden='true' href='#using-taxonomic-properties-in-rules'></a>Using taxonomic properties in rules</h3>
<h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Using taxonomic properties in rules</h3>
<p>There is one exception in variables used for the rules: all column names of the <a href='microorganisms.html'>microorganisms</a> data set can also be used, but do not have to exist in the data set. These column names are: <code>mo</code>, <code>fullname</code>, <code>kingdom</code>, <code>phylum</code>, <code>class</code>, <code>order</code>, <code>family</code>, <code>genus</code>, <code>species</code>, <code>subspecies</code>, <code>rank</code>, <code>ref</code>, <code>species_id</code>, <code>source</code>, <code>prevalence</code> and <code>snomed</code>. Thus, this next example will work as well, despite the fact that the <code>df</code> data set does not contain a column <code>genus</code>:</p><pre class='sourceCode r'><code><span class='va'>y</span> <span class='op'>&lt;-</span> <span class='fu'>custom_eucast_rules</span><span class='op'>(</span><span class='va'>TZP</span> <span class='op'>==</span> <span class='st'>"S"</span> <span class='op'>&amp;</span> <span class='va'>genus</span> <span class='op'>==</span> <span class='st'>"Klebsiella"</span> <span class='op'>~</span> <span class='va'>aminopenicillins</span> <span class='op'>==</span> <span class='st'>"S"</span>,
<p>There is one exception in variables used for the rules: all column names of the <a href='microorganisms.html'>microorganisms</a> data set can also be used, but do not have to exist in the data set. These column names are: <code>mo</code>, <code>fullname</code>, <code>kingdom</code>, <code>phylum</code>, <code>class</code>, <code>order</code>, <code>family</code>, <code>genus</code>, <code>species</code>, <code>subspecies</code>, <code>rank</code>, <code>ref</code>, <code>species_id</code>, <code>source</code>, <code>prevalence</code> and <code>snomed</code>. Thus, this next example will work as well, despite the fact that the <code>df</code> data set does not contain a column <code>genus</code>:</p><pre><span class='va'>y</span> <span class='op'>&lt;-</span> <span class='fu'>custom_eucast_rules</span><span class='op'>(</span><span class='va'>TZP</span> <span class='op'>==</span> <span class='st'>"S"</span> <span class='op'>&amp;</span> <span class='va'>genus</span> <span class='op'>==</span> <span class='st'>"Klebsiella"</span> <span class='op'>~</span> <span class='va'>aminopenicillins</span> <span class='op'>==</span> <span class='st'>"S"</span>,
<span class='va'>TZP</span> <span class='op'>==</span> <span class='st'>"R"</span> <span class='op'>&amp;</span> <span class='va'>genus</span> <span class='op'>==</span> <span class='st'>"Klebsiella"</span> <span class='op'>~</span> <span class='va'>aminopenicillins</span> <span class='op'>==</span> <span class='st'>"R"</span><span class='op'>)</span>
<span class='fu'><a href='eucast_rules.html'>eucast_rules</a></span><span class='op'>(</span><span class='va'>df</span>, rules <span class='op'>=</span> <span class='st'>"custom"</span>, custom_rules <span class='op'>=</span> <span class='va'>y</span><span class='op'>)</span>
<span class='co'>#&gt; mo TZP amox AMP</span>
<span class='co'>#&gt; 1 E. coli R </span>
<span class='co'>#&gt; 2 K. pneumoniae R R R</span>
</code></pre>
</pre>
<h3 class='hasAnchor' id='usage-of-antibiotic-group-names'><a class='anchor' aria-hidden='true' href='#usage-of-antibiotic-group-names'></a>Usage of antibiotic group names</h3>
<h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Usage of antibiotic group names</h3>
<p>It is possible to define antibiotic groups instead of single antibiotics for the rule consequence, the part <em>after</em> the tilde. In above examples, the antibiotic group <code>aminopenicillins</code> is used to include ampicillin and amoxicillin. The following groups are allowed (case-insensitive). Within parentheses are the agents that will be matched when running the rule.</p><ul>
@ -348,12 +340,13 @@
</ul>
<h2 class="hasAnchor" id="maturing-lifecycle"><a class="anchor" href="#maturing-lifecycle"></a>Maturing Lifecycle</h2>
<h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable Lifecycle</h2>
<p><img src='figures/lifecycle_maturing.svg' style=margin-bottom:5px /> <br />
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing</strong>. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome <a href='https://github.com/msberends/AMR/issues'>to suggest changes at our repository</a> or <a href='AMR.html'>write us an email (see section 'Contact Us')</a>.</p>
<p><img src='figures/lifecycle_stable.svg' style=margin-bottom:5px /> <br />
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, a argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on Our Website!</h2>
@ -361,7 +354,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<div class="ref-examples sourceCode"><pre class='sourceCode r'><code><span class='va'>x</span> <span class='op'>&lt;-</span> <span class='fu'>custom_eucast_rules</span><span class='op'>(</span><span class='va'>AMC</span> <span class='op'>==</span> <span class='st'>"R"</span> <span class='op'>&amp;</span> <span class='va'>genus</span> <span class='op'>==</span> <span class='st'>"Klebsiella"</span> <span class='op'>~</span> <span class='va'>aminopenicillins</span> <span class='op'>==</span> <span class='st'>"R"</span>,
<pre class="examples"><span class='va'>x</span> <span class='op'>&lt;-</span> <span class='fu'>custom_eucast_rules</span><span class='op'>(</span><span class='va'>AMC</span> <span class='op'>==</span> <span class='st'>"R"</span> <span class='op'>&amp;</span> <span class='va'>genus</span> <span class='op'>==</span> <span class='st'>"Klebsiella"</span> <span class='op'>~</span> <span class='va'>aminopenicillins</span> <span class='op'>==</span> <span class='st'>"R"</span>,
<span class='va'>AMC</span> <span class='op'>==</span> <span class='st'>"I"</span> <span class='op'>&amp;</span> <span class='va'>genus</span> <span class='op'>==</span> <span class='st'>"Klebsiella"</span> <span class='op'>~</span> <span class='va'>aminopenicillins</span> <span class='op'>==</span> <span class='st'>"I"</span><span class='op'>)</span>
<span class='fu'><a href='eucast_rules.html'>eucast_rules</a></span><span class='op'>(</span><span class='va'>example_isolates</span>,
rules <span class='op'>=</span> <span class='st'>"custom"</span>,
@ -372,7 +365,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
<span class='va'>x2</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='va'>x</span>,
<span class='fu'>custom_eucast_rules</span><span class='op'>(</span><span class='va'>TZP</span> <span class='op'>==</span> <span class='st'>"R"</span> <span class='op'>~</span> <span class='va'>carbapenems</span> <span class='op'>==</span> <span class='st'>"R"</span><span class='op'>)</span><span class='op'>)</span>
<span class='va'>x2</span>
</code></pre></div>
</pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<nav id="toc" data-toggle="toc" class="sticky-top">
@ -384,11 +377,11 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
<footer>
<div class="copyright">
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, Christian F. Luz.</p></p>
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
</div>
<div class="pkgdown">
<p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 1.6.1.9001.</p></p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
</div>
</footer>
@ -397,8 +390,6 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
</body>
</html>

9
docs/reference/eucast_rules.html
View File

@ -86,7 +86,7 @@ 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="Latest development version">1.7.1.9053</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9054</span>
</span>
</div>
@ -247,7 +247,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
rules <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/options.html'>getOption</a></span><span class='op'>(</span><span class='st'>"AMR_eucastrules"</span>, default <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"breakpoints"</span>, <span class='st'>"expert"</span><span class='op'>)</span><span class='op'>)</span>,
verbose <span class='op'>=</span> <span class='cn'>FALSE</span>,
version_breakpoints <span class='op'>=</span> <span class='fl'>11</span>,
version_expertrules <span class='op'>=</span> <span class='fl'>3.2</span>,
version_expertrules <span class='op'>=</span> <span class='fl'>3.3</span>,
ampc_cephalosporin_resistance <span class='op'>=</span> <span class='cn'>NA</span>,
only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span>,
custom_rules <span class='op'>=</span> <span class='cn'>NULL</span>,
@ -285,7 +285,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
</tr>
<tr>
<th>version_expertrules</th>
<td><p>the version number to use for the EUCAST Expert Rules and Intrinsic Resistance guideline. Can be either "3.2" or "3.1".</p></td>
<td><p>the version number to use for the EUCAST Expert Rules and Intrinsic Resistance guideline. Can be either "3.3", "3.2" or "3.1".</p></td>
</tr>
<tr>
<th>ampc_cephalosporin_resistance</th>
@ -321,6 +321,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility testing.</strong> <em>Clin Microbiol Infect.</em> 2013;19(2):141-60; doi: <a href='https://doi.org/10.1111/j.1469-0691.2011.03703.x'>10.1111/j.1469-0691.2011.03703.x</a></p></li>
<li><p>EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes Tables. Version 3.1, 2016. <a href='https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf'>(link)</a></p></li>
<li><p>EUCAST Intrinsic Resistance and Unusual Phenotypes. Version 3.2, 2020. <a href='https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/2020/Intrinsic_Resistance_and_Unusual_Phenotypes_Tables_v3.2_20200225.pdf'>(link)</a></p></li>
<li><p>EUCAST Intrinsic Resistance and Unusual Phenotypes. Version 3.3, 2021. <a href='https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/2021/Intrinsic_Resistance_and_Unusual_Phenotypes_Tables_v3.3_20211018.pdf'>(link)</a></p></li>
<li><p>EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 9.0, 2019. <a href='https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_9.0_Breakpoint_Tables.xlsx'>(link)</a></p></li>
<li><p>EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 10.0, 2020. <a href='https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_10.0_Breakpoint_Tables.xlsx'>(link)</a></p></li>
<li><p>EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 11.0, 2021. <a href='https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_11.0_Breakpoint_Tables.xlsx'>(link)</a></p></li>
@ -434,7 +435,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<footer>
<div class="copyright">
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, Dennis Souverein, Erwin E. A. Hassing, Christian F. Luz.</p>
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
</div>
<div class="pkgdown">

10
docs/reference/index.html
View File

@ -84,7 +84,7 @@
</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="Latest development version">1.7.1.9053</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9054</span>
</span>
</div>
@ -322,19 +322,19 @@
<tr>
<td>
<p><code><a href="as.rsi.html">as.rsi()</a></code> <code><a href="as.rsi.html">is.rsi()</a></code> <code><a href="as.rsi.html">is.rsi.eligible()</a></code> </p>
<p><code><a href="as.rsi.html">as.rsi()</a></code> <code><a href="as.rsi.html">NA_rsi_</a></code> <code><a href="as.rsi.html">is.rsi()</a></code> <code><a href="as.rsi.html">is.rsi.eligible()</a></code> </p>
</td>
<td><p>Interpret MIC and Disk Values, or Clean Raw R/SI Data</p></td>
</tr><tr>
<td>
<p><code><a href="as.mic.html">as.mic()</a></code> <code><a href="as.mic.html">is.mic()</a></code> </p>
<p><code><a href="as.mic.html">as.mic()</a></code> <code><a href="as.mic.html">NA_mic_</a></code> <code><a href="as.mic.html">is.mic()</a></code> </p>
</td>
<td><p>Transform Input to Minimum Inhibitory Concentrations (MIC)</p></td>
</tr><tr>
<td>
<p><code><a href="as.disk.html">as.disk()</a></code> <code><a href="as.disk.html">is.disk()</a></code> </p>
<p><code><a href="as.disk.html">as.disk()</a></code> <code><a href="as.disk.html">NA_disk_</a></code> <code><a href="as.disk.html">is.disk()</a></code> </p>
</td>
<td><p>Transform Input to Disk Diffusion Diameters</p></td>
</tr><tr>
@ -681,7 +681,7 @@
<footer>
<div class="copyright">
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, Dennis Souverein, Erwin E. A. Hassing, Christian F. Luz.</p>
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
</div>
<div class="pkgdown">

33
docs/reference/italicise_taxonomy.html
View File

@ -58,8 +58,6 @@
<!-- mathjax -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
@ -71,15 +69,9 @@
</head>
<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
@ -93,7 +85,7 @@
</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="Latest development version">1.7.1.9040</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9054</span>
</span>
</div>
@ -238,7 +230,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>Italicise Taxonomic Families, Genera, Species, Subspecies</h1>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/main/R/italicise_taxonomy.R'><code>R/italicise_taxonomy.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/italicise_taxonomy.R'><code>R/italicise_taxonomy.R</code></a></small>
<div class="hidden name"><code>italicise_taxonomy.Rd</code></div>
</div>
@ -246,9 +238,9 @@
<p>According to the binomial nomenclature, the lowest four taxonomic levels (family, genus, species, subspecies) should be printed in italic. This function finds taxonomic names within strings and makes them italic.</p>
</div>
<div class="ref-usage sourceCode"><pre class='sourceCode r'><code><span class='fu'>italicise_taxonomy</span><span class='op'>(</span><span class='va'>string</span>, type <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"markdown"</span>, <span class='st'>"ansi"</span><span class='op'>)</span><span class='op'>)</span>
<pre class="usage"><span class='fu'>italicise_taxonomy</span><span class='op'>(</span><span class='va'>string</span>, type <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"markdown"</span>, <span class='st'>"ansi"</span><span class='op'>)</span><span class='op'>)</span>
<span class='fu'>italicize_taxonomy</span><span class='op'>(</span><span class='va'>string</span>, type <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"markdown"</span>, <span class='st'>"ansi"</span><span class='op'>)</span><span class='op'>)</span></code></pre></div>
<span class='fu'>italicize_taxonomy</span><span class='op'>(</span><span class='va'>string</span>, type <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"markdown"</span>, <span class='st'>"ansi"</span><span class='op'>)</span><span class='op'>)</span></pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@ -268,12 +260,13 @@
<p>This function finds the taxonomic names and makes them italic based on the <a href='microorganisms.html'>microorganisms</a> data set.</p>
<p>The taxonomic names can be italicised using markdown (the default) by adding <code><a href='https://rdrr.io/r/base/Arithmetic.html'>*</a></code> before and after the taxonomic names, or using ANSI colours by adding <code>\033[3m</code> before and <code>\033[23m</code> after the taxonomic names. If multiple ANSI colours are not available, no conversion will occur.</p>
<p>This function also supports abbreviation of the genus if it is followed by a species, such as "E. coli" and "K. pneumoniae ozaenae".</p>
<h2 class="hasAnchor" id="maturing-lifecycle"><a class="anchor" href="#maturing-lifecycle"></a>Maturing Lifecycle</h2>
<h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable Lifecycle</h2>
<p><img src='figures/lifecycle_maturing.svg' style=margin-bottom:5px /> <br />
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing</strong>. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome <a href='https://github.com/msberends/AMR/issues'>to suggest changes at our repository</a> or <a href='AMR.html'>write us an email (see section 'Contact Us')</a>.</p>
<p><img src='figures/lifecycle_stable.svg' style=margin-bottom:5px /> <br />
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, a argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on Our Website!</h2>
@ -281,7 +274,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<div class="ref-examples sourceCode"><pre class='sourceCode r'><code><span class='fu'>italicise_taxonomy</span><span class='op'>(</span><span class='st'>"An overview of Staphylococcus aureus isolates"</span><span class='op'>)</span>
<pre class="examples"><span class='fu'>italicise_taxonomy</span><span class='op'>(</span><span class='st'>"An overview of Staphylococcus aureus isolates"</span><span class='op'>)</span>
<span class='fu'>italicise_taxonomy</span><span class='op'>(</span><span class='st'>"An overview of S. aureus isolates"</span><span class='op'>)</span>
<span class='fu'><a href='https://rdrr.io/r/base/cat.html'>cat</a></span><span class='op'>(</span><span class='fu'>italicise_taxonomy</span><span class='op'>(</span><span class='st'>"An overview of S. aureus isolates"</span>, type <span class='op'>=</span> <span class='st'>"ansi"</span><span class='op'>)</span><span class='op'>)</span>
@ -295,7 +288,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/theme.html'>theme</a></span><span class='op'>(</span>plot.title <span class='op'>=</span> <span class='fu'>ggtext</span><span class='fu'>::</span><span class='fu'><a href='https://wilkelab.org/ggtext/reference/element_markdown.html'>element_markdown</a></span><span class='op'>(</span><span class='op'>)</span><span class='op'>)</span>
<span class='op'>}</span>
<span class='co'># }</span>
</code></pre></div>
</pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<nav id="toc" data-toggle="toc" class="sticky-top">
@ -307,11 +300,11 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
<footer>
<div class="copyright">
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, Christian F. Luz.</p></p>
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
</div>
<div class="pkgdown">
<p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 1.6.1.9001.</p></p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
</div>
</footer>
@ -320,8 +313,6 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
</body>
</html>

23
docs/reference/plot.html
View File

@ -85,7 +85,7 @@
</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="Latest development version">1.7.1.9053</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9054</span>
</span>
</div>
@ -254,7 +254,7 @@
<span class='op'>)</span>
<span class='co'># S3 method for mic</span>
<span class='fu'>autoplot</span><span class='op'>(</span>
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/autoplot.html'>autoplot</a></span><span class='op'>(</span>
<span class='va'>object</span>,
mo <span class='op'>=</span> <span class='cn'>NULL</span>,
ab <span class='op'>=</span> <span class='cn'>NULL</span>,
@ -269,7 +269,7 @@
<span class='op'>)</span>
<span class='co'># S3 method for mic</span>
<span class='fu'>fortify</span><span class='op'>(</span><span class='va'>object</span>, <span class='va'>...</span><span class='op'>)</span>
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/fortify.html'>fortify</a></span><span class='op'>(</span><span class='va'>object</span>, <span class='va'>...</span><span class='op'>)</span>
<span class='co'># S3 method for disk</span>
<span class='fu'>plot</span><span class='op'>(</span>
@ -287,7 +287,7 @@
<span class='op'>)</span>
<span class='co'># S3 method for disk</span>
<span class='fu'>autoplot</span><span class='op'>(</span>
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/autoplot.html'>autoplot</a></span><span class='op'>(</span>
<span class='va'>object</span>,
mo <span class='op'>=</span> <span class='cn'>NULL</span>,
ab <span class='op'>=</span> <span class='cn'>NULL</span>,
@ -302,7 +302,7 @@
<span class='op'>)</span>
<span class='co'># S3 method for disk</span>
<span class='fu'>fortify</span><span class='op'>(</span><span class='va'>object</span>, <span class='va'>...</span><span class='op'>)</span>
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/fortify.html'>fortify</a></span><span class='op'>(</span><span class='va'>object</span>, <span class='va'>...</span><span class='op'>)</span>
<span class='co'># S3 method for rsi</span>
<span class='fu'>plot</span><span class='op'>(</span>
@ -314,7 +314,7 @@
<span class='op'>)</span>
<span class='co'># S3 method for rsi</span>
<span class='fu'>autoplot</span><span class='op'>(</span>
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/autoplot.html'>autoplot</a></span><span class='op'>(</span>
<span class='va'>object</span>,
title <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span><span class='op'>(</span><span class='st'>"Resistance Overview of"</span>, <span class='fu'><a href='https://rdrr.io/r/base/deparse.html'>deparse</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/substitute.html'>substitute</a></span><span class='op'>(</span><span class='va'>object</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span>,
xlab <span class='op'>=</span> <span class='st'>"Antimicrobial Interpretation"</span>,
@ -325,7 +325,7 @@
<span class='op'>)</span>
<span class='co'># S3 method for rsi</span>
<span class='fu'>fortify</span><span class='op'>(</span><span class='va'>object</span>, <span class='va'>...</span><span class='op'>)</span></pre>
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/fortify.html'>fortify</a></span><span class='op'>(</span><span class='va'>object</span>, <span class='va'>...</span><span class='op'>)</span></pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@ -381,12 +381,13 @@
<p>The interpretation of "I" will be named "Increased exposure" for all EUCAST guidelines since 2019, and will be named "Intermediate" in all other cases.</p>
<p>For interpreting MIC values as well as disk diffusion diameters, supported guidelines to be used as input for the <code>guideline</code> argument are: "EUCAST 2021", "EUCAST 2020", "EUCAST 2019", "EUCAST 2018", "EUCAST 2017", "EUCAST 2016", "EUCAST 2015", "EUCAST 2014", "EUCAST 2013", "EUCAST 2012", "EUCAST 2011", "CLSI 2020", "CLSI 2019", "CLSI 2018", "CLSI 2017", "CLSI 2016", "CLSI 2015", "CLSI 2014", "CLSI 2013", "CLSI 2012", "CLSI 2011" and "CLSI 2010".</p>
<p>Simply using <code>"CLSI"</code> or <code>"EUCAST"</code> as input will automatically select the latest version of that guideline.</p>
<h2 class="hasAnchor" id="maturing-lifecycle"><a class="anchor" href="#maturing-lifecycle"></a>Maturing Lifecycle</h2>
<h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable Lifecycle</h2>
<p><img src='figures/lifecycle_maturing.svg' style=margin-bottom:5px /> <br />
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing</strong>. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome <a href='https://github.com/msberends/AMR/issues'>to suggest changes at our repository</a> or <a href='AMR.html'>write us an email (see section 'Contact Us')</a>.</p>
<p><img src='figures/lifecycle_stable.svg' style=margin-bottom:5px /> <br />
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, a argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on Our Website!</h2>
@ -425,7 +426,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
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<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, Dennis Souverein, Erwin E. A. Hassing, Christian F. Luz.</p>
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
</div>
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