CI tests

docs/reference/count.html

@@ -258,7 +258,7 @@ count_R and count_IR can be used to count resistant isolates, count_S and count_
 <span class='fu'>n_rsi</span>(<span class='no'>...</span>)
 
 <span class='fu'>count_df</span>(<span class='no'>data</span>, <span class='kw'>translate_ab</span> <span class='kw'>=</span> <span class='st'>"name"</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(),
-  <span class='kw'>combine_IR</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
+  <span class='kw'>combine_SI</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>combine_IR</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
     <table class="ref-arguments">
@@ -284,8 +284,8 @@ count_R and count_IR can be used to count resistant isolates, count_S and count_
       <td><p>language of the returned text, defaults to system language (see <code><a href='translate.html'>get_locale</a></code>) and can also be set with <code><a href='https://www.rdocumentation.org/packages/base/topics/options'>getOption</a>("AMR_locale")</code>. Use <code>language = NULL</code> or <code>language = ""</code> to prevent translation.</p></td>
     </tr>
     <tr>
-      <th>combine_IR</th>
-      <td><p>a logical to indicate whether all values of I and R must be merged into one, so the output only consists of S vs. IR (susceptible vs. non-susceptible)</p></td>
+      <th>combine_SI</th>
+      <td><p>a logical to indicate whether all values of I and S must be merged into one, so the output only consists of S+I vs. R (susceptible vs. resistant). This used to be the parameter <code>combine_IR</code>, but this now follows the redefinition by EUCAST about the interpretion of I (increased exposure) in 2019, see below. Default is now <code>TRUE</code>.</p></td>
     </tr>
     </table>
     
@@ -303,6 +303,19 @@ count_R and count_IR can be used to count resistant isolates, count_S and count_
 <p><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_S(...) + count_IR(...)</code>.</p>
 <p><code>count_df</code> takes any variable from <code>data</code> that has an <code>"rsi"</code> class (created with <code><a href='as.rsi.html'>as.rsi</a></code>) and counts the amounts of R, I and S. The resulting <em>tidy data</em> (see Source) <code>data.frame</code> will have three rows (S/I/R) and a column for each variable with class <code>"rsi"</code>.</p>
     
+    <h2 class="hasAnchor" id="interpretation-of-s-i-and-r"><a class="anchor" href="#interpretation-of-s-i-and-r"></a>Interpretation of S, I and R</h2>
+
+    
+    <p>In 2019, EUCAST has decided to change the definitions of susceptibility testing categories S, I and R as shown below. Results of several consultations on the new definitions are available on the EUCAST website under "Consultations".</p>
+<ul>
+<li><p><strong>S</strong>Susceptible, standard dosing regimen: A microorganism is categorised as "Susceptible, standard dosing regimen", when there is a high likelihood of therapeutic success using a standard dosing regimen of the agent.</p></li>
+<li><p><strong>I</strong>Susceptible, increased exposure: A microorganism is categorised as "Susceptible, Increased exposure" when there is a high likelihood of therapeutic success because exposure to the agent is increased by adjusting the dosing regimen or by its concentration at the site of infection.</p></li>
+<li><p><strong>R</strong>Resistant: A microorganism is categorised as "Resistant" when there is a high likelihood of therapeutic failure even when there is increased exposure.</p></li>
+</ul>
+    <p>Exposure is a function of how the mode of administration, dose, dosing interval, infusion time, as well as distribution and excretion of the antimicrobial agent will influence the infecting organism at the site of infection.</p>
+<p>Source: <a href='http://www.eucast.org/newsiandr/'>http://www.eucast.org/newsiandr/</a>.</p>
+<p><strong>This AMR package honours this new insight.</strong></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>
 
     
@@ -384,6 +397,8 @@ count_R and count_IR can be used to count resistant isolates, count_S and count_
 
       <li><a href="#details">Details</a></li>
 
+      <li><a href="#interpretation-of-s-i-and-r">Interpretation of S, I and R</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>