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(v0.9.0.9008) Happy new year! Add lifecycles

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dr. M.S. (Matthijs) Berends
2020-01-05 17:22:09 +01:00
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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">0.9.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9007</span>
</span>
</div>
@ -252,6 +252,12 @@
<span class='fu'>portion_df</span>(<span class='no'>...</span>)</pre>
<h2 class="hasAnchor" id="retired-lifecycle"><a class="anchor" href="#retired-lifecycle"></a>Retired lifecycle</h2>
<p><img src='figures/lifecycle_retired.svg' style=margin-bottom:5px /> <br />
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>retired</strong>. A retired function is no longer under active development, and (if appropiate) a better alternative is available. We will only make the necessary changes to ensure that retired functions remain available. No new arguments will be added, and only the most critical bugs will be fixed.</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>
@ -262,6 +268,7 @@
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#retired-lifecycle">Retired lifecycle</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
</ul>
@ -271,7 +278,7 @@
<footer>
<div class="copyright">
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N M Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
</div>
<div class="pkgdown">

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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">0.9.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9007</span>
</span>
</div>
@ -305,6 +305,12 @@
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>All output will be <a href='translate.html'>translate</a>d where possible.</p>
<h2 class="hasAnchor" id="maturing-lifecycle"><a class="anchor" href="#maturing-lifecycle"></a>Maturing 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. We will strive to maintain backward compatibility, but the function needs wider usage and more extensive testing in order to optimise the unlying code.</p>
<h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>
@ -358,6 +364,7 @@
<li><a href="#arguments">Arguments</a></li>
<li><a href="#value">Value</a></li>
<li><a href="#details">Details</a></li>
<li><a href="#maturing-lifecycle">Maturing lifecycle</a></li>
<li><a href="#source">Source</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
<li><a href="#see-also">See also</a></li>
@ -370,7 +377,7 @@
<footer>
<div class="copyright">
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N M Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
</div>
<div class="pkgdown">

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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">0.9.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9007</span>
</span>
</div>
@ -263,6 +263,13 @@
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>An integer (no decimals) if <code>exact = FALSE</code>, a double (with decimals) otherwise</p>
<h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable lifecycle</h2>
<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, we are largely happy with the unlying code, and major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; we will avoid removing arguments or changing the meaning of existing arguments.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. To begin with, the function or argument will be deprecated; it will 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>
@ -287,6 +294,7 @@
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
<li><a href="#value">Value</a></li>
<li><a href="#stable-lifecycle">Stable lifecycle</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
<li><a href="#see-also">See also</a></li>
<li><a href="#examples">Examples</a></li>
@ -298,7 +306,7 @@
<footer>
<div class="copyright">
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N M Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
</div>
<div class="pkgdown">

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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">0.9.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9007</span>
</span>
</div>
@ -272,6 +272,13 @@ The default is to split on young children (0-11), youth (12-24), young adults (2
</ul></li>
</ul>
<h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable lifecycle</h2>
<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, we are largely happy with the unlying code, and major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; we will avoid removing arguments or changing the meaning of existing arguments.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. To begin with, the function or argument will be deprecated; it will 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>
@ -320,6 +327,7 @@ The default is to split on young children (0-11), youth (12-24), young adults (2
<li><a href="#arguments">Arguments</a></li>
<li><a href="#value">Value</a></li>
<li><a href="#details">Details</a></li>
<li><a href="#stable-lifecycle">Stable lifecycle</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
<li><a href="#see-also">See also</a></li>
<li><a href="#examples">Examples</a></li>
@ -331,7 +339,7 @@ The default is to split on young children (0-11), youth (12-24), young adults (2
<footer>
<div class="copyright">
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N M Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
</div>
<div class="pkgdown">

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@ -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">0.9.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9007</span>
</span>
</div>
@ -268,6 +268,12 @@
<p>World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology: <a href='https://www.whocc.no/atc_ddd_index/'>https://www.whocc.no/atc_ddd_index/</a></p>
<p>WHONET 2019 software: <a href='http://www.whonet.org/software.html'>http://www.whonet.org/software.html</a></p>
<p>European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: <a href='http://ec.europa.eu/health/documents/community-register/html/atc.htm'>http://ec.europa.eu/health/documents/community-register/html/atc.htm</a></p>
<h2 class="hasAnchor" id="maturing-lifecycle"><a class="anchor" href="#maturing-lifecycle"></a>Maturing 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. We will strive to maintain backward compatibility, but the function needs wider usage and more extensive testing in order to optimise the unlying code.</p>
<h2 class="hasAnchor" id="whocc"><a class="anchor" href="#whocc"></a>WHOCC</h2>
@ -311,6 +317,7 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
<li><a href="#value">Value</a></li>
<li><a href="#details">Details</a></li>
<li><a href="#source">Source</a></li>
<li><a href="#maturing-lifecycle">Maturing lifecycle</a></li>
<li><a href="#whocc">WHOCC</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
<li><a href="#see-also">See also</a></li>
@ -323,7 +330,7 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
<footer>
<div class="copyright">
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N M Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
</div>
<div class="pkgdown">

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@ -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">0.9.0.9006</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9007</span>
</span>
</div>
@ -260,6 +260,13 @@
<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>
<h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable lifecycle</h2>
<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, we are largely happy with the unlying code, and major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; we will avoid removing arguments or changing the meaning of existing arguments.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. To begin with, the function or argument will be deprecated; it will 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>
@ -286,6 +293,7 @@
<li><a href="#arguments">Arguments</a></li>
<li><a href="#value">Value</a></li>
<li><a href="#details">Details</a></li>
<li><a href="#stable-lifecycle">Stable lifecycle</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
<li><a href="#see-also">See also</a></li>
<li><a href="#examples">Examples</a></li>

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@ -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">0.9.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9007</span>
</span>
</div>
@ -260,6 +260,13 @@
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>To interpret MIC values as RSI values, use <code><a href='as.rsi.html'>as.rsi()</a></code> on MIC values. It supports guidelines from EUCAST and CLSI.</p>
<h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable lifecycle</h2>
<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, we are largely happy with the unlying code, and major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; we will avoid removing arguments or changing the meaning of existing arguments.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. To begin with, the function or argument will be deprecated; it will 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>
@ -296,6 +303,7 @@
<li><a href="#arguments">Arguments</a></li>
<li><a href="#value">Value</a></li>
<li><a href="#details">Details</a></li>
<li><a href="#stable-lifecycle">Stable lifecycle</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
<li><a href="#see-also">See also</a></li>
<li><a href="#examples">Examples</a></li>
@ -307,7 +315,7 @@
<footer>
<div class="copyright">
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N M Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
</div>
<div class="pkgdown">

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@ -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">0.9.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9007</span>
</span>
</div>
@ -371,6 +371,13 @@
<li><p>Catalogue of Life: Annual Checklist (public online taxonomic database), <a href='http://www.catalogueoflife.org'>http://www.catalogueoflife.org</a> (check included annual version with <code><a href='catalogue_of_life_version.html'>catalogue_of_life_version()</a></code>).</p></li>
</ol>
<h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable lifecycle</h2>
<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, we are largely happy with the unlying code, and major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; we will avoid removing arguments or changing the meaning of existing arguments.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. To begin with, the function or argument will be deprecated; it will 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="catalogue-of-life"><a class="anchor" href="#catalogue-of-life"></a>Catalogue of Life</h2>
@ -451,6 +458,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
<li><a href="#value">Value</a></li>
<li><a href="#details">Details</a></li>
<li><a href="#source">Source</a></li>
<li><a href="#stable-lifecycle">Stable lifecycle</a></li>
<li><a href="#catalogue-of-life">Catalogue of Life</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
<li><a href="#see-also">See also</a></li>
@ -463,7 +471,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
<footer>
<div class="copyright">
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N M Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
</div>
<div class="pkgdown">

12
docs/reference/as.rsi.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">0.9.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9007</span>
</span>
</div>
@ -307,6 +307,13 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
</ul>
<p>This AMR package honours this new insight. Use <code><a href='proportion.html'>susceptibility()</a></code> (equal to <code><a href='proportion.html'>proportion_SI()</a></code>) to determine antimicrobial susceptibility and <code><a href='count.html'>count_susceptible()</a></code> (equal to <code><a href='count.html'>count_SI()</a></code>) to count susceptible isolates.</p>
<h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable lifecycle</h2>
<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, we are largely happy with the unlying code, and major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; we will avoid removing arguments or changing the meaning of existing arguments.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. To begin with, the function or argument will be deprecated; it will 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>
@ -360,6 +367,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
<li><a href="#value">Value</a></li>
<li><a href="#details">Details</a></li>
<li><a href="#interpretation-of-r-and-s-i">Interpretation of R and S/I</a></li>
<li><a href="#stable-lifecycle">Stable lifecycle</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
<li><a href="#see-also">See also</a></li>
<li><a href="#examples">Examples</a></li>
@ -371,7 +379,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
<footer>
<div class="copyright">
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N M Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
</div>
<div class="pkgdown">

11
docs/reference/atc_online.html
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@ -86,7 +86,7 @@ This function requires an internet connection." />
</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">0.9.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9008</span>
</span>
</div>
@ -304,6 +304,12 @@ This function requires an internet connection." />
<li><p><code>"ml"</code> = milliliter (e.g. eyedrops)</p></li>
</ul>
<h2 class="hasAnchor" id="questioning-lifecycle"><a class="anchor" href="#questioning-lifecycle"></a>Questioning lifecycle</h2>
<p><img src='figures/lifecycle_questioning.svg' style=margin-bottom:5px /> <br />
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>questioning</strong>. We are no longer convinced that this function is the optimal approach (but we do not know yet what a better approach would be), or whether this function should be in our <code>AMR</code> package at all.</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>
@ -330,6 +336,7 @@ This function requires an internet connection." />
<li><a href="#arguments">Arguments</a></li>
<li><a href="#source">Source</a></li>
<li><a href="#details">Details</a></li>
<li><a href="#questioning-lifecycle">Questioning lifecycle</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
<li><a href="#examples">Examples</a></li>
</ul>
@ -340,7 +347,7 @@ This function requires an internet connection." />
<footer>
<div class="copyright">
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N M Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
</div>
<div class="pkgdown">

16
docs/reference/availability.html
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@ -51,7 +51,7 @@
<script src="../extra.js"></script>
<meta property="og:title" content="Check availability of columns — availability" />
<meta property="og:description" content="Easy check for availability of columns in a data set. This makes it easy to get an idea of which antimicrobial combination can be used for calculation with e.g. resistance()." />
<meta property="og:description" content="Easy check for data availability of all columns in a data set. This makes it easy to get an idea of which antimicrobial combinations can be used for calculation with e.g. susceptibility() and resistance()." />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.png" />
<meta name="twitter:card" content="summary" />
@ -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">0.9.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9007</span>
</span>
</div>
@ -234,7 +234,7 @@
</div>
<div class="ref-description">
<p>Easy check for availability of columns in a data set. This makes it easy to get an idea of which antimicrobial combination can be used for calculation with e.g. <code><a href='proportion.html'>resistance()</a></code>.</p>
<p>Easy check for data availability of all columns in a data set. This makes it easy to get an idea of which antimicrobial combinations can be used for calculation with e.g. <code><a href='proportion.html'>susceptibility()</a></code> and <code><a href='proportion.html'>resistance()</a></code>.</p>
</div>
<pre class="usage"><span class='fu'>availability</span>(<span class='no'>tbl</span>, <span class='kw'>width</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
@ -258,6 +258,13 @@
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>The function returns a <code><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></code> with columns <code>"resistant"</code> and <code>"visual_resistance"</code>. The values in that columns are calculated with <code><a href='proportion.html'>resistance()</a></code>.</p>
<h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable lifecycle</h2>
<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, we are largely happy with the unlying code, and major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; we will avoid removing arguments or changing the meaning of existing arguments.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. To begin with, the function or argument will be deprecated; it will 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>
@ -285,6 +292,7 @@
<li><a href="#arguments">Arguments</a></li>
<li><a href="#value">Value</a></li>
<li><a href="#details">Details</a></li>
<li><a href="#stable-lifecycle">Stable lifecycle</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
<li><a href="#examples">Examples</a></li>
</ul>
@ -295,7 +303,7 @@
<footer>
<div class="copyright">
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N M Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
</div>
<div class="pkgdown">

12
docs/reference/bug_drug_combinations.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">0.9.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9007</span>
</span>
</div>
@ -324,6 +324,13 @@
<p>The function <code><a href='https://rdrr.io/r/base/format.html'>format()</a></code> calculates the resistance per bug-drug combination. Use <code>combine_IR = FALSE</code> (default) to test R vs. S+I and <code>combine_IR = TRUE</code> to test R+I vs. S.</p>
<p>The language of the output can be overwritten with <code><a href='https://rdrr.io/r/base/options.html'>options(AMR_locale)</a></code>, please see <a href='translate.html'>translate</a>.</p>
<h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable lifecycle</h2>
<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, we are largely happy with the unlying code, and major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; we will avoid removing arguments or changing the meaning of existing arguments.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. To begin with, the function or argument will be deprecated; it will 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>
@ -353,6 +360,7 @@
<li><a href="#source">Source</a></li>
<li><a href="#value">Value</a></li>
<li><a href="#details">Details</a></li>
<li><a href="#stable-lifecycle">Stable lifecycle</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
<li><a href="#examples">Examples</a></li>
</ul>
@ -363,7 +371,7 @@
<footer>
<div class="copyright">
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N M Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
</div>
<div class="pkgdown">

12
docs/reference/count.html
View File

@ -86,7 +86,7 @@ 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="Latest development version">0.9.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9007</span>
</span>
</div>
@ -307,6 +307,13 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
<p>The function <code>count_resistant()</code> is equal to the function <code>count_R()</code>. The function <code>count_susceptible()</code> is equal to the function <code>count_SI()</code>.</p>
<p>The function <code>n_rsi()</code> is an alias of <code>count_all()</code>. They can be used to count all available isolates, i.e. where all input antibiotics have an available result (S, I or R). Their use is equal to <code><a href='https://dplyr.tidyverse.org/reference/n_distinct.html'>n_distinct()</a></code>. Their function is equal to <code>count_susceptible(...) + count_resistant(...)</code>.</p>
<p>The function <code>count_df()</code> takes any variable from <code>data</code> that has an <code><a href='as.rsi.html'>rsi</a></code> class (created with <code><a href='as.rsi.html'>as.rsi()</a></code>) and counts the number of S's, I's and R's. The function <code><a href='proportion.html'>rsi_df()</a></code> works exactly like <code>count_df()</code>, but adds the percentage of S, I and R.</p>
<h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable lifecycle</h2>
<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, we are largely happy with the unlying code, and major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; we will avoid removing arguments or changing the meaning of existing arguments.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. To begin with, the function or argument will be deprecated; it will 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="interpretation-of-r-and-s-i"><a class="anchor" href="#interpretation-of-r-and-s-i"></a>Interpretation of R and S/I</h2>
@ -425,6 +432,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
<li><a href="#arguments">Arguments</a></li>
<li><a href="#value">Value</a></li>
<li><a href="#details">Details</a></li>
<li><a href="#stable-lifecycle">Stable lifecycle</a></li>
<li><a href="#interpretation-of-r-and-s-i">Interpretation of R and S/I</a></li>
<li><a href="#combination-therapy">Combination therapy</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
@ -438,7 +446,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
<footer>
<div class="copyright">
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N M Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
</div>
<div class="pkgdown">

11
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">0.9.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9007</span>
</span>
</div>
@ -395,6 +395,12 @@ To <em>not</em> use these rules, please use <code>eucast_rules(..., rules = c("b
<strong>TMP</strong>: trimethoprim (<a href='https://www.whocc.no/atc_ddd_index/?code=J01EA01'>J01EA01</a>),
<strong>SXT</strong>: trimethoprim/sulfamethoxazole (<a href='https://www.whocc.no/atc_ddd_index/?code=J01EE01'>J01EE01</a>),
<strong>VAN</strong>: vancomycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XA01'>J01XA01</a>).</p>
<h2 class="hasAnchor" id="maturing-lifecycle"><a class="anchor" href="#maturing-lifecycle"></a>Maturing 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. We will strive to maintain backward compatibility, but the function needs wider usage and more extensive testing in order to optimise the unlying code.</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>
@ -451,6 +457,7 @@ To <em>not</em> use these rules, please use <code>eucast_rules(..., rules = c("b
<li><a href="#value">Value</a></li>
<li><a href="#details">Details</a></li>
<li><a href="#antibiotics">Antibiotics</a></li>
<li><a href="#maturing-lifecycle">Maturing lifecycle</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
<li><a href="#examples">Examples</a></li>
</ul>
@ -461,7 +468,7 @@ To <em>not</em> use these rules, please use <code>eucast_rules(..., rules = c("b
<footer>
<div class="copyright">
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N M Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
</div>
<div class="pkgdown">

12
docs/reference/extended-functions.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">0.9.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9007</span>
</span>
</div>
@ -242,6 +242,13 @@
<span class='fu'>scale_type.ab</span>(<span class='no'>x</span>)</pre>
<h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable lifecycle</h2>
<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, we are largely happy with the unlying code, and major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; we will avoid removing arguments or changing the meaning of existing arguments.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. To begin with, the function or argument will be deprecated; it will 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>
@ -252,6 +259,7 @@
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#stable-lifecycle">Stable lifecycle</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
</ul>
@ -261,7 +269,7 @@
<footer>
<div class="copyright">
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N M Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
</div>
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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">0.9.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9007</span>
</span>
</div>
@ -291,6 +291,13 @@
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>The <code>group</code> column in <a href='antibiotics.html'>antibiotics</a> data set will be searched for <code>ab_class</code> (case-insensitive). If no results are found, the <code>atc_group1</code> and <code>atc_group2</code> columns will be searched. Next, <code>x</code> will be checked for column names with a value in any abbreviations, codes or official names found in the <a href='antibiotics.html'>antibiotics</a> data set.</p>
<h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable lifecycle</h2>
<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, we are largely happy with the unlying code, and major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; we will avoid removing arguments or changing the meaning of existing arguments.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. To begin with, the function or argument will be deprecated; it will 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="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>dplyr</span>)
@ -327,6 +334,7 @@
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
<li><a href="#details">Details</a></li>
<li><a href="#stable-lifecycle">Stable lifecycle</a></li>
<li><a href="#examples">Examples</a></li>
</ul>
@ -336,7 +344,7 @@
<footer>
<div class="copyright">
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N M Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
</div>
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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">0.9.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9008</span>
</span>
</div>
@ -327,6 +327,12 @@
<p>where <code>df</code> are the degrees of freedom.</p>
<p>If there are more than two categories and you want to find out which ones are significantly different from their null expectation, you can use the same method of testing each category vs. the sum of all categories, with the Bonferroni correction. You use <em>G</em>-tests for each category, of course.</p>
<h2 class="hasAnchor" id="questioning-lifecycle"><a class="anchor" href="#questioning-lifecycle"></a>Questioning lifecycle</h2>
<p><img src='figures/lifecycle_questioning.svg' style=margin-bottom:5px /> <br />
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>questioning</strong>. We are no longer convinced that this function is the optimal approach (but we do not know yet what a better approach would be), or whether this function should be in our <code>AMR</code> package at all.</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>
@ -383,6 +389,7 @@
<li><a href="#source">Source</a></li>
<li><a href="#value">Value</a></li>
<li><a href="#details">Details</a></li>
<li><a href="#questioning-lifecycle">Questioning lifecycle</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
<li><a href="#references">References</a></li>
<li><a href="#see-also">See also</a></li>
@ -395,7 +402,7 @@
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<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N M Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
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<p><code>labels_rsi_count()</code> print datalabels on the bars with percentage and amount of isolates using <code><a href='https://ggplot2.tidyverse.org/reference/geom_text.html'>ggplot2::geom_text()</a></code></p>
<p><code>ggplot_rsi()</code> is a wrapper around all above functions that uses data as first input. This makes it possible to use this function after a pipe (<code>%&gt;%</code>). See Examples.</p>
<h2 class="hasAnchor" id="maturing-lifecycle"><a class="anchor" href="#maturing-lifecycle"></a>Maturing 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. We will strive to maintain backward compatibility, but the function needs wider usage and more extensive testing in order to optimise the unlying code.</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>
@ -511,6 +517,7 @@
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
<li><a href="#details">Details</a></li>
<li><a href="#maturing-lifecycle">Maturing lifecycle</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
<li><a href="#examples">Examples</a></li>
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@ -521,7 +528,7 @@
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<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N M Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
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<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>You can look for an antibiotic (trade) name or abbreviation and it will search <code>x</code> and the <a href='antibiotics.html'>antibiotics</a> data set for any column containing a name or code of that antibiotic. <strong>Longer columns names take precendence over shorter column names.</strong></p>
<h2 class="hasAnchor" id="maturing-lifecycle"><a class="anchor" href="#maturing-lifecycle"></a>Maturing 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. We will strive to maintain backward compatibility, but the function needs wider usage and more extensive testing in order to optimise the unlying code.</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>
@ -303,6 +309,7 @@
<li><a href="#arguments">Arguments</a></li>
<li><a href="#value">Value</a></li>
<li><a href="#details">Details</a></li>
<li><a href="#maturing-lifecycle">Maturing lifecycle</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
<li><a href="#examples">Examples</a></li>
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@ -313,7 +320,7 @@
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<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N M Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9007</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0</span>
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@ -273,6 +273,13 @@
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p><strong>Note:</strong> As opposed to the <code><a href='https://dplyr.tidyverse.org/reference/join.html'>dplyr::join()</a></code> functions of <code>dplyr</code>, <code><a href='https://rdrr.io/r/base/character.html'>character</a></code> vectors are supported and at default existing columns will get a suffix <code>"2"</code> and the newly joined columns will not get a suffix. See <code><a href='https://dplyr.tidyverse.org/reference/join.html'>dplyr::join()</a></code> for more information.</p>
<h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable lifecycle</h2>
<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, we are largely happy with the unlying code, and major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; we will avoid removing arguments or changing the meaning of existing arguments.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. To begin with, the function or argument will be deprecated; it will 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>
@ -301,6 +308,7 @@
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
<li><a href="#details">Details</a></li>
<li><a href="#stable-lifecycle">Stable lifecycle</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
<li><a href="#examples">Examples</a></li>
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@ -311,7 +319,7 @@
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<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N M Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
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@ -358,6 +358,13 @@
</ul>
<p>The function <code>key_antibiotics_equal()</code> checks the characters returned by <code>key_antibiotics()</code> for equality, and returns a <code><a href='https://rdrr.io/r/base/logical.html'>logical</a></code> vector.</p>
<h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable lifecycle</h2>
<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, we are largely happy with the unlying code, and major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; we will avoid removing arguments or changing the meaning of existing arguments.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. To begin with, the function or argument will be deprecated; it will 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="key-antibiotics"><a class="anchor" href="#key-antibiotics"></a>Key antibiotics</h2>
@ -413,6 +420,7 @@
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
<li><a href="#details">Details</a></li>
<li><a href="#stable-lifecycle">Stable lifecycle</a></li>
<li><a href="#key-antibiotics">Key antibiotics</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
<li><a href="#see-also">See also</a></li>
@ -425,7 +433,7 @@
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<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N M Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0</span>
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@ -261,6 +261,12 @@
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<h2 class="hasAnchor" id="questioning-lifecycle"><a class="anchor" href="#questioning-lifecycle"></a>Questioning lifecycle</h2>
<p><img src='figures/lifecycle_questioning.svg' style=margin-bottom:5px /> <br />
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>questioning</strong>. We are no longer convinced that this function is the optimal approach (but we do not know yet what a better approach would be), or whether this function should be in our <code>AMR</code> package at all.</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>
@ -275,6 +281,7 @@
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
<li><a href="#questioning-lifecycle">Questioning lifecycle</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
<li><a href="#see-also">See also</a></li>
</ul>
@ -285,7 +292,7 @@
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<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N M Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
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<h1>Lifecycles of functions in the <code>AMR</code> package</h1>
<div class="hidden name"><code>lifecycle.Rd</code></div>
</div>
<div class="ref-description">
<p>Our functions are categorised using <a href='https://www.tidyverse.org/lifecycle'>the lifecycle circle of the <code>tidyverse</code> as found on www.tidyverse.org/lifecycle</a>.</p>
<p><img src='figures/lifecycle_tidyverse.svg' height=200px style=margin-bottom:5px /> <br />
This page contains a section for every lifecycle (with text borrowed from the aforementioned <code>tidyverse</code> website), so they can be used in the manual pages of our functions.</p>
</div>
<h2 class="hasAnchor" id="experimental-lifecycle"><a class="anchor" href="#experimental-lifecycle"></a>Experimental lifecycle</h2>
<p><img src='figures/lifecycle_experimental.svg' style=margin-bottom:5px /> <br />
The lifecycle of this function is <strong>experimental</strong>. An experimental function is in the very early stages of development. The unlying code might be changing frequently as we rapidly iterate and explore variations in search of the best fit. Experimental functions might be removed without deprecation, so you are generally best off waiting until a function is more mature before you use it in production code. Experimental functions will not be included in releases we submit to CRAN.</p>
<h2 class="hasAnchor" id="maturing-lifecycle"><a class="anchor" href="#maturing-lifecycle"></a>Maturing lifecycle</h2>
<p><img src='figures/lifecycle_maturing.svg' style=margin-bottom:5px /> <br />
The lifecycle of this function is <strong>maturing</strong>. The unlying code of a maturing function has been roughed out, but finer details might still change. We will strive to maintain backward compatibility, but the function needs wider usage and more extensive testing in order to optimise the unlying code.</p>
<h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable lifecycle</h2>
<p><img src='figures/lifecycle_stable.svg' style=margin-bottom:5px /> <br />
The lifecycle of this function is <strong>stable</strong>. In a stable function, we are largely happy with the unlying code, and major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; we will avoid removing arguments or changing the meaning of existing arguments.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. To begin with, the function or argument will be deprecated; it will 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="retired-lifecycle"><a class="anchor" href="#retired-lifecycle"></a>Retired lifecycle</h2>
<p><img src='figures/lifecycle_retired.svg' style=margin-bottom:5px /> <br />
The lifecycle of this function is <strong>retired</strong>. A retired function is no longer under active development, and (if appropiate) a better alternative is available. We will only make the necessary changes to ensure that retired functions remain available. No new arguments will be added, and only the most critical bugs will be fixed.</p>
<h2 class="hasAnchor" id="archived-lifecycle"><a class="anchor" href="#archived-lifecycle"></a>Archived lifecycle</h2>
<p><img src='figures/lifecycle_archived.svg' style=margin-bottom:5px /> <br />
The lifecycle of this function is <strong>archived</strong>. The development of an archived function has ended, and it is no longer available in future package versions.</p>
<h2 class="hasAnchor" id="dormant-lifecycle"><a class="anchor" href="#dormant-lifecycle"></a>Dormant lifecycle</h2>
<p><img src='figures/lifecycle_dormant.svg' style=margin-bottom:5px /> <br />
The lifecycle of this function is <strong>dormant</strong>. A dormant function is currently not under active development and has not reached a stable phase. We might return to it in the future. As with experimental functions, you are best off waiting until a function is more mature before you use it in production code.</p>
<h2 class="hasAnchor" id="questioning-lifecycle"><a class="anchor" href="#questioning-lifecycle"></a>Questioning lifecycle</h2>
<p><img src='figures/lifecycle_questioning.svg' style=margin-bottom:5px /> <br />
The lifecycle of this function is <strong>questioning</strong>. We are no longer convinced that this function is the optimal approach (but we do not know yet what a better approach would be), or whether this function should be in our <code>AMR</code> package at all.</p>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#experimental-lifecycle">Experimental lifecycle</a></li>
<li><a href="#maturing-lifecycle">Maturing lifecycle</a></li>
<li><a href="#stable-lifecycle">Stable lifecycle</a></li>
<li><a href="#retired-lifecycle">Retired lifecycle</a></li>
<li><a href="#archived-lifecycle">Archived lifecycle</a></li>
<li><a href="#dormant-lifecycle">Dormant lifecycle</a></li>
<li><a href="#questioning-lifecycle">Questioning lifecycle</a></li>
</ul>
</div>
</div>
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<div class="copyright">
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N M Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
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16
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@ -51,7 +51,7 @@
<script src="../extra.js"></script>
<meta property="og:title" content="Pattern Matching — like" />
<meta property="og:description" content="Convenient wrapper around base::grep() to match a pattern: a %like% b. It always returns a logical vector and is always case-insensitive (use a %like_case% b for case-sensitive matching). Also, pattern (b) can be as long as x (a) to compare items of each index in both vectors, or can both have the same length to iterate over all cases." />
<meta property="og:description" content="Convenient wrapper around base::grep() to match a pattern: a %like% b. It always returns a logical vector and is always case-insensitive (use a %like_case% b for case-sensitive matching). Also, pattern (b) can be as long as x (a) to compare items of each index in both vectors, or they both can have the same length to iterate over all cases." />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.png" />
<meta name="twitter:card" content="summary" />
@ -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">0.9.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9007</span>
</span>
</div>
@ -234,7 +234,7 @@
</div>
<div class="ref-description">
<p>Convenient wrapper around <code><a href='https://rdrr.io/r/base/grep.html'>base::grep()</a></code> to match a pattern: <code>a %like% b</code>. It always returns a <code><a href='https://rdrr.io/r/base/logical.html'>logical</a></code> vector and is always case-insensitive (use <code>a %like_case% b</code> for case-sensitive matching). Also, <code>pattern</code> (<em>b</em>) can be as long as <code>x</code> (<em>a</em>) to compare items of each index in both vectors, or can both have the same length to iterate over all cases.</p>
<p>Convenient wrapper around <code><a href='https://rdrr.io/r/base/grep.html'>base::grep()</a></code> to match a pattern: <code>a %like% b</code>. It always returns a <code><a href='https://rdrr.io/r/base/logical.html'>logical</a></code> vector and is always case-insensitive (use <code>a %like_case% b</code> for case-sensitive matching). Also, <code>pattern</code> (<em>b</em>) can be as long as <code>x</code> (<em>a</em>) to compare items of each index in both vectors, or they both can have the same length to iterate over all cases.</p>
</div>
<pre class="usage"><span class='fu'>like</span>(<span class='no'>x</span>, <span class='no'>pattern</span>, <span class='kw'>ignore.case</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
@ -269,6 +269,13 @@
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>Using RStudio? This function can also be inserted from the Addins menu and can have its own Keyboard Shortcut like <code>Ctrl+Shift+L</code> or <code>Cmd+Shift+L</code> (see <code>Tools</code> &gt; <code>Modify Keyboard Shortcuts...</code>).</p>
<h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable lifecycle</h2>
<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, we are largely happy with the unlying code, and major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; we will avoid removing arguments or changing the meaning of existing arguments.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. To begin with, the function or argument will be deprecated; it will 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>
@ -306,6 +313,7 @@
<li><a href="#source">Source</a></li>
<li><a href="#value">Value</a></li>
<li><a href="#details">Details</a></li>
<li><a href="#stable-lifecycle">Stable lifecycle</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
<li><a href="#see-also">See also</a></li>
<li><a href="#examples">Examples</a></li>
@ -317,7 +325,7 @@
<footer>
<div class="copyright">
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N M Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
</div>
<div class="pkgdown">

11
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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">0.9.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9007</span>
</span>
</div>
@ -330,6 +330,12 @@ The Dutch national guideline - Rijksinstituut voor Volksgezondheid en Milieu "WI
<p>Please suggest your own (country-specific) guidelines by letting us know: <a href='https://gitlab.com/msberends/AMR/issues/new'>https://gitlab.com/msberends/AMR/issues/new</a>.</p>
<p><strong>Note:</strong> Every test that involves the Enterobacteriaceae family, will internally be performed using its newly named order Enterobacterales, since the Enterobacteriaceae family has been taxonomically reclassified by Adeolu <em>et al.</em> in 2016. Before that, Enterobacteriaceae was the only family under the Enterobacteriales (with an i) order. All species under the old Enterobacteriaceae family are still under the new Enterobacterales (without an i) order, but divided into multiple families. The way tests are performed now by this <code>mdro()</code> function makes sure that results from before 2016 and after 2016 are identical.</p>
<h2 class="hasAnchor" id="maturing-lifecycle"><a class="anchor" href="#maturing-lifecycle"></a>Maturing 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. We will strive to maintain backward compatibility, but the function needs wider usage and more extensive testing in order to optimise the unlying code.</p>
<h2 class="hasAnchor" id="antibiotics"><a class="anchor" href="#antibiotics"></a>Antibiotics</h2>
@ -456,6 +462,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
<li><a href="#source">Source</a></li>
<li><a href="#value">Value</a></li>
<li><a href="#details">Details</a></li>
<li><a href="#maturing-lifecycle">Maturing lifecycle</a></li>
<li><a href="#antibiotics">Antibiotics</a></li>
<li><a href="#interpretation-of-r-and-s-i">Interpretation of R and S/I</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
@ -468,7 +475,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
<footer>
<div class="copyright">
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N M Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
</div>
<div class="pkgdown">

12
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View File

@ -86,7 +86,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
</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">0.9.0.9002</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9007</span>
</span>
</div>
@ -306,6 +306,13 @@ mo_genus("lab_Staph_aureus")
</pre>
<h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable lifecycle</h2>
<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, we are largely happy with the unlying code, and major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; we will avoid removing arguments or changing the meaning of existing arguments.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. To begin with, the function or argument will be deprecated; it will 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>
@ -318,6 +325,7 @@ mo_genus("lab_Staph_aureus")
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
<li><a href="#details">Details</a></li>
<li><a href="#stable-lifecycle">Stable lifecycle</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
</ul>
@ -327,7 +335,7 @@ mo_genus("lab_Staph_aureus")
<footer>
<div class="copyright">
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N M Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
</div>
<div class="pkgdown">

11
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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">0.9.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9008</span>
</span>
</div>
@ -255,6 +255,12 @@
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>Text</p>
<h2 class="hasAnchor" id="questioning-lifecycle"><a class="anchor" href="#questioning-lifecycle"></a>Questioning lifecycle</h2>
<p><img src='figures/lifecycle_questioning.svg' style=margin-bottom:5px /> <br />
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>questioning</strong>. We are no longer convinced that this function is the optimal approach (but we do not know yet what a better approach would be), or whether this function should be in our <code>AMR</code> package at all.</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>
@ -267,6 +273,7 @@
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
<li><a href="#value">Value</a></li>
<li><a href="#questioning-lifecycle">Questioning lifecycle</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
</ul>
@ -276,7 +283,7 @@
<footer>
<div class="copyright">
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N M Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
</div>
<div class="pkgdown">

12
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View File

@ -86,7 +86,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
</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">0.9.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9007</span>
</span>
</div>
@ -357,6 +357,13 @@ resistance() should be used to calculate resistance, susceptibility() should be
</pre>
<p>Using <code>only_all_tested</code> has no impact when only using one antibiotic as input.</p>
<h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable lifecycle</h2>
<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, we are largely happy with the unlying code, and major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; we will avoid removing arguments or changing the meaning of existing arguments.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. To begin with, the function or argument will be deprecated; it will 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="interpretation-of-r-and-s-i"><a class="anchor" href="#interpretation-of-r-and-s-i"></a>Interpretation of R and S/I</h2>
@ -470,6 +477,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
<li><a href="#value">Value</a></li>
<li><a href="#details">Details</a></li>
<li><a href="#combination-therapy">Combination therapy</a></li>
<li><a href="#stable-lifecycle">Stable lifecycle</a></li>
<li><a href="#interpretation-of-r-and-s-i">Interpretation of R and S/I</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
<li><a href="#see-also">See also</a></li>
@ -482,7 +490,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
<footer>
<div class="copyright">
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N M Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
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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">0.9.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9007</span>
</span>
</div>
@ -393,6 +393,12 @@
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>Column names will be transformed, but the original column names are set as a "label" attribute and can be seen in e.g. RStudio Viewer.</p>
<h2 class="hasAnchor" id="dormant-lifecycle"><a class="anchor" href="#dormant-lifecycle"></a>Dormant lifecycle</h2>
<p><img src='figures/lifecycle_dormant.svg' style=margin-bottom:5px /> <br />
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>dormant</strong>. A dormant function is currently not under active development and has not reached a stable phase. We might return to it in the future. As with experimental functions, you are best off waiting until a function is more mature before you use it in production code.</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>
@ -405,6 +411,7 @@
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
<li><a href="#details">Details</a></li>
<li><a href="#dormant-lifecycle">Dormant lifecycle</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
</ul>
@ -414,7 +421,7 @@
<footer>
<div class="copyright">
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N M Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
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@ -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">0.9.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9007</span>
</span>
</div>
@ -359,6 +359,12 @@
<li><p><code>"lin"</code> or <code>"linear"</code>: a linear regression model</p></li>
</ul>
<h2 class="hasAnchor" id="maturing-lifecycle"><a class="anchor" href="#maturing-lifecycle"></a>Maturing 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. We will strive to maintain backward compatibility, but the function needs wider usage and more extensive testing in order to optimise the unlying code.</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>
@ -439,6 +445,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
<li><a href="#arguments">Arguments</a></li>
<li><a href="#value">Value</a></li>
<li><a href="#details">Details</a></li>
<li><a href="#maturing-lifecycle">Maturing lifecycle</a></li>
<li><a href="#interpretation-of-r-and-s-i">Interpretation of R and S/I</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
<li><a href="#see-also">See also</a></li>
@ -451,7 +458,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
<footer>
<div class="copyright">
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N M Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
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@ -86,7 +86,7 @@ When negative: the left tail is longer; the mass of the distribution is concentr
</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">0.9.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9008</span>
</span>
</div>
@ -263,6 +263,12 @@ When negative: the left tail is longer; the mass of the distribution is concentr
</tr>
</table>
<h2 class="hasAnchor" id="questioning-lifecycle"><a class="anchor" href="#questioning-lifecycle"></a>Questioning lifecycle</h2>
<p><img src='figures/lifecycle_questioning.svg' style=margin-bottom:5px /> <br />
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>questioning</strong>. We are no longer convinced that this function is the optimal approach (but we do not know yet what a better approach would be), or whether this function should be in our <code>AMR</code> package at all.</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>
@ -277,6 +283,7 @@ When negative: the left tail is longer; the mass of the distribution is concentr
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
<li><a href="#questioning-lifecycle">Questioning lifecycle</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
<li><a href="#see-also">See also</a></li>
</ul>
@ -287,7 +294,7 @@ When negative: the left tail is longer; the mass of the distribution is concentr
<footer>
<div class="copyright">
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N M Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
</div>
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@ -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">0.9.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9007</span>
</span>
</div>
@ -247,6 +247,13 @@
<p>Please suggest your own translations <a href='https://gitlab.com/msberends/AMR/issues/new?issue[title]=Translation%20suggestion'>by creating a new issue on our repository</a>.</p>
<p>This file will be read by all functions where a translated output can be desired, like all <code><a href='mo_property.html'>mo_property()</a></code> functions (<code><a href='mo_property.html'>mo_fullname()</a></code>, <code><a href='mo_property.html'>mo_type()</a></code>, etc.).</p>
<p>The system language will be used at default, if that language is supported. The system language can be overwritten with <code><a href='https://rdrr.io/r/base/Sys.setenv.html'>Sys.setenv(AMR_locale = yourlanguage)</a></code>.</p>
<h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable lifecycle</h2>
<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, we are largely happy with the unlying code, and major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; we will avoid removing arguments or changing the meaning of existing arguments.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. To begin with, the function or argument will be deprecated; it will 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>
@ -286,6 +293,7 @@
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#details">Details</a></li>
<li><a href="#stable-lifecycle">Stable lifecycle</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
<li><a href="#examples">Examples</a></li>
</ul>
@ -296,7 +304,7 @@
<footer>
<div class="copyright">
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N M Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
</div>
<div class="pkgdown">