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

docs/reference/plot.html

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