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(v1.6.0.9048) ab selectors overhaul

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dr. M.S. (Matthijs) Berends committed 2021-05-19 22:55:42 +02:00
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docs/reference/AMR-deprecated.html
+134 -2
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@@ -82,7 +82,7 @@
</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">1.6.0.9015</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9048</span>
</span>
</div>
@@ -239,7 +239,7 @@
</div>
<div class="ref-description">
<p>These functions are so-called '<a href='https://rdrr.io/r/base/Deprecated.html'>Deprecated</a>'. They will be removed in a future release. Using the functions will give a warning with the name of the function it has been replaced by (if there is one).</p>
<p>These functions are so-called '<a href='https://rdrr.io/r/base/Deprecated.html'>Deprecated</a>'. <strong>They will be removed in a future release.</strong> Using the functions will give a warning with the name of the function it has been replaced by (if there is one).</p>
</div>
<pre class="usage"><span class='fu'>p_symbol</span><span class='op'>(</span><span class='va'>p</span>, emptychar <span class='op'>=</span> <span class='st'>" "</span><span class='op'>)</span>
@@ -286,9 +286,141 @@
info <span class='op'>=</span> <span class='cn'>FALSE</span>,
na.rm <span class='op'>=</span> <span class='cn'>TRUE</span>,
<span class='va'>...</span>
<span class='op'>)</span>
<span class='fu'>filter_ab_class</span><span class='op'>(</span>
<span class='va'>x</span>,
<span class='va'>ab_class</span>,
result <span class='op'>=</span> <span class='cn'>NULL</span>,
scope <span class='op'>=</span> <span class='st'>"any"</span>,
only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span>,
<span class='va'>...</span>
<span class='op'>)</span>
<span class='fu'>filter_aminoglycosides</span><span class='op'>(</span>
<span class='va'>x</span>,
result <span class='op'>=</span> <span class='cn'>NULL</span>,
scope <span class='op'>=</span> <span class='st'>"any"</span>,
only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span>,
<span class='va'>...</span>
<span class='op'>)</span>
<span class='fu'>filter_betalactams</span><span class='op'>(</span>
<span class='va'>x</span>,
result <span class='op'>=</span> <span class='cn'>NULL</span>,
scope <span class='op'>=</span> <span class='st'>"any"</span>,
only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span>,
<span class='va'>...</span>
<span class='op'>)</span>
<span class='fu'>filter_carbapenems</span><span class='op'>(</span>
<span class='va'>x</span>,
result <span class='op'>=</span> <span class='cn'>NULL</span>,
scope <span class='op'>=</span> <span class='st'>"any"</span>,
only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span>,
<span class='va'>...</span>
<span class='op'>)</span>
<span class='fu'>filter_cephalosporins</span><span class='op'>(</span>
<span class='va'>x</span>,
result <span class='op'>=</span> <span class='cn'>NULL</span>,
scope <span class='op'>=</span> <span class='st'>"any"</span>,
only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span>,
<span class='va'>...</span>
<span class='op'>)</span>
<span class='fu'>filter_1st_cephalosporins</span><span class='op'>(</span>
<span class='va'>x</span>,
result <span class='op'>=</span> <span class='cn'>NULL</span>,
scope <span class='op'>=</span> <span class='st'>"any"</span>,
only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span>,
<span class='va'>...</span>
<span class='op'>)</span>
<span class='fu'>filter_2nd_cephalosporins</span><span class='op'>(</span>
<span class='va'>x</span>,
result <span class='op'>=</span> <span class='cn'>NULL</span>,
scope <span class='op'>=</span> <span class='st'>"any"</span>,
only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span>,
<span class='va'>...</span>
<span class='op'>)</span>
<span class='fu'>filter_3rd_cephalosporins</span><span class='op'>(</span>
<span class='va'>x</span>,
result <span class='op'>=</span> <span class='cn'>NULL</span>,
scope <span class='op'>=</span> <span class='st'>"any"</span>,
only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span>,
<span class='va'>...</span>
<span class='op'>)</span>
<span class='fu'>filter_4th_cephalosporins</span><span class='op'>(</span>
<span class='va'>x</span>,
result <span class='op'>=</span> <span class='cn'>NULL</span>,
scope <span class='op'>=</span> <span class='st'>"any"</span>,
only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span>,
<span class='va'>...</span>
<span class='op'>)</span>
<span class='fu'>filter_5th_cephalosporins</span><span class='op'>(</span>
<span class='va'>x</span>,
result <span class='op'>=</span> <span class='cn'>NULL</span>,
scope <span class='op'>=</span> <span class='st'>"any"</span>,
only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span>,
<span class='va'>...</span>
<span class='op'>)</span>
<span class='fu'>filter_fluoroquinolones</span><span class='op'>(</span>
<span class='va'>x</span>,
result <span class='op'>=</span> <span class='cn'>NULL</span>,
scope <span class='op'>=</span> <span class='st'>"any"</span>,
only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span>,
<span class='va'>...</span>
<span class='op'>)</span>
<span class='fu'>filter_glycopeptides</span><span class='op'>(</span>
<span class='va'>x</span>,
result <span class='op'>=</span> <span class='cn'>NULL</span>,
scope <span class='op'>=</span> <span class='st'>"any"</span>,
only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span>,
<span class='va'>...</span>
<span class='op'>)</span>
<span class='fu'>filter_macrolides</span><span class='op'>(</span>
<span class='va'>x</span>,
result <span class='op'>=</span> <span class='cn'>NULL</span>,
scope <span class='op'>=</span> <span class='st'>"any"</span>,
only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span>,
<span class='va'>...</span>
<span class='op'>)</span>
<span class='fu'>filter_oxazolidinones</span><span class='op'>(</span>
<span class='va'>x</span>,
result <span class='op'>=</span> <span class='cn'>NULL</span>,
scope <span class='op'>=</span> <span class='st'>"any"</span>,
only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span>,
<span class='va'>...</span>
<span class='op'>)</span>
<span class='fu'>filter_penicillins</span><span class='op'>(</span>
<span class='va'>x</span>,
result <span class='op'>=</span> <span class='cn'>NULL</span>,
scope <span class='op'>=</span> <span class='st'>"any"</span>,
only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span>,
<span class='va'>...</span>
<span class='op'>)</span>
<span class='fu'>filter_tetracyclines</span><span class='op'>(</span>
<span class='va'>x</span>,
result <span class='op'>=</span> <span class='cn'>NULL</span>,
scope <span class='op'>=</span> <span class='st'>"any"</span>,
only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span>,
<span class='va'>...</span>
<span class='op'>)</span></pre>
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>All antibiotic class selectors (such as <code><a href='antibiotic_class_selectors.html'>carbapenems()</a></code>, <code><a href='antibiotic_class_selectors.html'>aminoglycosides()</a></code>) can now be used for filtering as well, making all their accompanying <code>filter_*()</code> functions redundant (such as <code>filter_carbapenems()</code>, <code>filter_aminoglycosides()</code>).</p>
<h2 class="hasAnchor" id="retired-lifecycle"><a class="anchor" href="#retired-lifecycle"></a>Retired Lifecycle</h2>
docs/reference/antibiotic_class_selectors.html
+45 -12
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@@ -49,7 +49,7 @@
<script src="../extra.js"></script>
<meta property="og:title" content="Antibiotic Class Selectors — antibiotic_class_selectors" />
<meta property="og:description" content="These functions help to select the columns of antibiotics that are of a specific antibiotic class, without the need to define the columns or antibiotic abbreviations.
<meta property="og:description" content="These functions help to filter and select columns with antibiotic test results that are of a specific antibiotic class, without the need to define the columns or antibiotic abbreviations.
" />
<meta property="og:image" content="https://msberends.github.io/AMR/logo.png" />
@@ -83,7 +83,7 @@
</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">1.6.0.9047</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9048</span>
</span>
</div>
@@ -240,7 +240,7 @@
</div>
<div class="ref-description">
<p>These functions help to select the columns of antibiotics that are of a specific antibiotic class, without the need to define the columns or antibiotic abbreviations. <strong>
<p>These functions help to filter and select columns with antibiotic test results that are of a specific antibiotic class, without the need to define the columns or antibiotic abbreviations. <strong>
</strong></p>
</div>
@@ -293,7 +293,8 @@
<p><strong>
</strong></p>
<p>All columns will be searched for known antibiotic names, abbreviations, brand names and codes (ATC, EARS-Net, WHO, etc.) in the <a href='antibiotics.html'>antibiotics</a> data set. This means that a selector like e.g. <code>aminoglycosides()</code> will pick up column names like 'gen', 'genta', 'J01GB03', 'tobra', 'Tobracin', etc.</p>
<p>These functions can be used in data set calls for selecting columns and filtering rows, see <em>Examples</em>. They support base R, but work more convenient in dplyr functions such as <code><a href='https://dplyr.tidyverse.org/reference/select.html'>select()</a></code>, <code><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter()</a></code> and <code><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise()</a></code>.</p>
<p>All columns in the data in which these functions are called will be searched for known antibiotic names, abbreviations, brand names, and codes (ATC, EARS-Net, WHO, etc.) in the <a href='antibiotics.html'>antibiotics</a> data set. This means that a selector like e.g. <code>aminoglycosides()</code> will pick up column names like 'gen', 'genta', 'J01GB03', 'tobra', 'Tobracin', etc.</p>
<p>The group of betalactams consists of all carbapenems, cephalosporins and penicillins.</p>
<h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable Lifecycle</h2>
@@ -312,19 +313,36 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
<div class='dont-index'><p><code><a href='filter_ab_class.html'>filter_ab_class()</a></code> for the <code><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter()</a></code> equivalent.</p></div>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='co'># `example_isolates` is a data set available in the AMR package.</span>
<span class='co'># See ?example_isolates.</span>
<span class='co'># this will select columns 'IPM' (imipenem) and 'MEM' (meropenem):</span>
<span class='co'># Base R ------------------------------------------------------------------</span>
<span class='co'># select columns 'IPM' (imipenem) and 'MEM' (meropenem)</span>
<span class='va'>example_isolates</span><span class='op'>[</span>, <span class='fu'>carbapenems</span><span class='op'>(</span><span class='op'>)</span><span class='op'>]</span>
<span class='co'># this will select columns 'mo', 'AMK', 'GEN', 'KAN' and 'TOB':</span>
<span class='co'># select columns 'mo', 'AMK', 'GEN', 'KAN' and 'TOB'</span>
<span class='va'>example_isolates</span><span class='op'>[</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"mo"</span>, <span class='fu'>aminoglycosides</span><span class='op'>(</span><span class='op'>)</span><span class='op'>)</span><span class='op'>]</span>
<span class='co'># filter using any() or all()</span>
<span class='va'>example_isolates</span><span class='op'>[</span><span class='fu'><a href='https://rdrr.io/r/base/any.html'>any</a></span><span class='op'>(</span><span class='fu'>carbapenems</span><span class='op'>(</span><span class='op'>)</span> <span class='op'>==</span> <span class='st'>"R"</span><span class='op'>)</span>, <span class='op'>]</span>
<span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span><span class='op'>(</span><span class='va'>example_isolates</span>, <span class='fu'><a href='https://rdrr.io/r/base/any.html'>any</a></span><span class='op'>(</span><span class='fu'>carbapenems</span><span class='op'>(</span><span class='op'>)</span> <span class='op'>==</span> <span class='st'>"R"</span><span class='op'>)</span><span class='op'>)</span>
<span class='co'># filter on any or all results in the carbapenem columns (i.e., IPM, MEM):</span>
<span class='va'>example_isolates</span><span class='op'>[</span><span class='fu'><a href='https://rdrr.io/r/base/any.html'>any</a></span><span class='op'>(</span><span class='fu'>carbapenems</span><span class='op'>(</span><span class='op'>)</span><span class='op'>)</span>, <span class='op'>]</span>
<span class='va'>example_isolates</span><span class='op'>[</span><span class='fu'><a href='https://rdrr.io/r/base/all.html'>all</a></span><span class='op'>(</span><span class='fu'>carbapenems</span><span class='op'>(</span><span class='op'>)</span><span class='op'>)</span>, <span class='op'>]</span>
<span class='co'># filter with multiple antibiotic selectors using c()</span>
<span class='va'>example_isolates</span><span class='op'>[</span><span class='fu'><a href='https://rdrr.io/r/base/all.html'>all</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fu'>carbapenems</span><span class='op'>(</span><span class='op'>)</span>, <span class='fu'>aminoglycosides</span><span class='op'>(</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>==</span> <span class='st'>"R"</span><span class='op'>)</span>, <span class='op'>]</span>
<span class='co'># filter + select in one go: get penicillins in carbapenems-resistant strains</span>
<span class='va'>example_isolates</span><span class='op'>[</span><span class='fu'><a href='https://rdrr.io/r/base/any.html'>any</a></span><span class='op'>(</span><span class='fu'>carbapenems</span><span class='op'>(</span><span class='op'>)</span> <span class='op'>==</span> <span class='st'>"R"</span><span class='op'>)</span>, <span class='fu'>penicillins</span><span class='op'>(</span><span class='op'>)</span><span class='op'>]</span>
<span class='co'># dplyr -------------------------------------------------------------------</span>
<span class='kw'>if</span> <span class='op'>(</span><span class='kw'><a href='https://rdrr.io/r/base/library.html'>require</a></span><span class='op'>(</span><span class='st'><a href='https://dplyr.tidyverse.org'>"dplyr"</a></span><span class='op'>)</span><span class='op'>)</span> <span class='op'>{</span>
<span class='co'># this will select columns 'IPM' (imipenem) and 'MEM' (meropenem):</span>
@@ -335,6 +353,20 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<span class='va'>example_isolates</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span><span class='op'>(</span><span class='va'>mo</span>, <span class='fu'>aminoglycosides</span><span class='op'>(</span><span class='op'>)</span><span class='op'>)</span>
<span class='co'># any() and all() work in dplyr's filter() too:</span>
<span class='va'>example_isolates</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/any.html'>any</a></span><span class='op'>(</span><span class='fu'>aminoglycosides</span><span class='op'>(</span><span class='op'>)</span> <span class='op'>==</span> <span class='st'>"R"</span><span class='op'>)</span>,
<span class='fu'><a href='https://rdrr.io/r/base/all.html'>all</a></span><span class='op'>(</span><span class='fu'>cephalosporins_2nd</span><span class='op'>(</span><span class='op'>)</span> <span class='op'>==</span> <span class='st'>"R"</span><span class='op'>)</span><span class='op'>)</span>
<span class='co'># also works with c():</span>
<span class='va'>example_isolates</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/any.html'>any</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fu'>carbapenems</span><span class='op'>(</span><span class='op'>)</span>, <span class='fu'>aminoglycosides</span><span class='op'>(</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>==</span> <span class='st'>"R"</span><span class='op'>)</span><span class='op'>)</span>
<span class='co'># not setting any/all will automatically apply all():</span>
<span class='va'>example_isolates</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span><span class='op'>(</span><span class='fu'>aminoglycosides</span><span class='op'>(</span><span class='op'>)</span> <span class='op'>==</span> <span class='st'>"R"</span><span class='op'>)</span>
<span class='co'>#&gt; i Assuming a filter on all 4 aminoglycosides.</span>
<span class='co'># this will select columns 'mo' and all antimycobacterial drugs ('RIF'):</span>
<span class='va'>example_isolates</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span><span class='op'>(</span><span class='va'>mo</span>, <span class='fu'>ab_class</span><span class='op'>(</span><span class='st'>"mycobact"</span><span class='op'>)</span><span class='op'>)</span>
@@ -353,10 +385,11 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span><span class='op'>(</span><span class='fu'>penicillins</span><span class='op'>(</span><span class='op'>)</span><span class='op'>)</span> <span class='co'># only the 'J01CA01' column will be selected</span>
<span class='co'># with dplyr 1.0.0 and higher (that adds 'across()'), this is equal:</span>
<span class='co'># with dplyr 1.0.0 and higher (that adds 'across()'), this is all equal:</span>
<span class='co'># (though the row names on the first are more correct)</span>
<span class='va'>example_isolates</span> <span class='op'>%&gt;%</span> <span class='fu'><a href='filter_ab_class.html'>filter_carbapenems</a></span><span class='op'>(</span><span class='st'>"R"</span>, <span class='st'>"all"</span><span class='op'>)</span>
<span class='va'>example_isolates</span> <span class='op'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span><span class='op'>(</span><span class='fu'><a href='https://dplyr.tidyverse.org/reference/across.html'>across</a></span><span class='op'>(</span><span class='fu'>carbapenems</span><span class='op'>(</span><span class='op'>)</span>, <span class='op'>~</span><span class='va'>.</span> <span class='op'>==</span> <span class='st'>"R"</span><span class='op'>)</span><span class='op'>)</span>
<span class='va'>example_isolates</span><span class='op'>[</span><span class='fu'>carbapenems</span><span class='op'>(</span><span class='op'>)</span> <span class='op'>==</span> <span class='st'>"R"</span>, <span class='op'>]</span>
<span class='va'>example_isolates</span> <span class='op'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span><span class='op'>(</span><span class='fu'>carbapenems</span><span class='op'>(</span><span class='op'>)</span> <span class='op'>==</span> <span class='st'>"R"</span><span class='op'>)</span>
<span class='va'>example_isolates</span> <span class='op'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span><span class='op'>(</span><span class='fu'><a href='https://dplyr.tidyverse.org/reference/across.html'>across</a></span><span class='op'>(</span><span class='fu'>carbapenems</span><span class='op'>(</span><span class='op'>)</span>, <span class='op'>~</span><span class='va'>.x</span> <span class='op'>==</span> <span class='st'>"R"</span><span class='op'>)</span><span class='op'>)</span>
<span class='op'>}</span>
</pre>
</div>
docs/reference/eucast_rules.html
+3 -3
View File
@@ -83,7 +83,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9021</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9048</span>
</span>
</div>
@@ -363,8 +363,8 @@ Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility test
<p>To define antibiotics column names, leave as it is to determine it automatically with <code><a href='guess_ab_col.html'>guess_ab_col()</a></code> or input a text (case-insensitive), or use <code>NULL</code> to skip a column (e.g. <code>TIC = NULL</code> to skip ticarcillin). Manually defined but non-existing columns will be skipped with a warning.</p>
<p>The following antibiotics are used for the functions <code>eucast_rules()</code> and <code><a href='mdro.html'>mdro()</a></code>. These are shown below in the format 'name (<code>antimicrobial ID</code>, <a href='https://www.whocc.no/atc/structure_and_principles/'>ATC code</a>)', sorted alphabetically:</p>
<p>Amikacin (<code>AMK</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01GB06&amp;showdescription=no'>J01GB06</a>), amoxicillin (<code>AMX</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA04&amp;showdescription=no'>J01CA04</a>), amoxicillin/clavulanic acid (<code>AMC</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CR02&amp;showdescription=no'>J01CR02</a>), ampicillin (<code>AMP</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA01&amp;showdescription=no'>J01CA01</a>), ampicillin/sulbactam (<code>SAM</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CR01&amp;showdescription=no'>J01CR01</a>), apalcillin (<code>APL</code>, no ATC code), aspoxicillin (<code>APX</code>, no ATC code), avibactam (<code>AVB</code>, no ATC code), avoparcin (<code>AVO</code>, no ATC code), azidocillin (<code>AZD</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CE04&amp;showdescription=no'>J01CE04</a>), azithromycin (<code>AZM</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01FA10&amp;showdescription=no'>J01FA10</a>), azlocillin (<code>AZL</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA09&amp;showdescription=no'>J01CA09</a>), aztreonam (<code>ATM</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DF01&amp;showdescription=no'>J01DF01</a>), bacampicillin (<code>BAM</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA06&amp;showdescription=no'>J01CA06</a>), benzylpenicillin (<code>PEN</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CE01&amp;showdescription=no'>J01CE01</a>), cadazolid (<code>CDZ</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD09&amp;showdescription=no'>J01DD09</a>), carbenicillin (<code>CRB</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA03&amp;showdescription=no'>J01CA03</a>), carindacillin (<code>CRN</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA05&amp;showdescription=no'>J01CA05</a>), cefacetrile (<code>CAC</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB10&amp;showdescription=no'>J01DB10</a>), cefaclor (<code>CEC</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC04&amp;showdescription=no'>J01DC04</a>), cefadroxil (<code>CFR</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB05&amp;showdescription=no'>J01DB05</a>), cefaloridine (<code>RID</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB02&amp;showdescription=no'>J01DB02</a>), cefamandole (<code>MAN</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC03&amp;showdescription=no'>J01DC03</a>), cefatrizine (<code>CTZ</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB07&amp;showdescription=no'>J01DB07</a>), cefazedone (<code>CZD</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB06&amp;showdescription=no'>J01DB06</a>), cefazolin (<code>CZO</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB04&amp;showdescription=no'>J01DB04</a>), cefcapene (<code>CCP</code>, no ATC code), cefcapene pivoxil (<code>CCX</code>, no ATC code), cefdinir (<code>CDR</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD15&amp;showdescription=no'>J01DD15</a>), cefditoren (<code>DIT</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD16&amp;showdescription=no'>J01DD16</a>), cefditoren pivoxil (<code>DIX</code>, no ATC code), cefepime (<code>FEP</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DE01&amp;showdescription=no'>J01DE01</a>), cefetamet (<code>CAT</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD10&amp;showdescription=no'>J01DD10</a>), cefetamet pivoxil (<code>CPI</code>, no ATC code), cefixime (<code>CFM</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD08&amp;showdescription=no'>J01DD08</a>), cefmenoxime (<code>CMX</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD05&amp;showdescription=no'>J01DD05</a>), cefmetazole (<code>CMZ</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC09&amp;showdescription=no'>J01DC09</a>), cefodizime (<code>DIZ</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD09&amp;showdescription=no'>J01DD09</a>), cefonicid (<code>CID</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC06&amp;showdescription=no'>J01DC06</a>), cefoperazone (<code>CFP</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD12&amp;showdescription=no'>J01DD12</a>), cefoperazone/sulbactam (<code>CSL</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD62&amp;showdescription=no'>J01DD62</a>), ceforanide (<code>CND</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC11&amp;showdescription=no'>J01DC11</a>), cefotaxime (<code>CTX</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD01&amp;showdescription=no'>J01DD01</a>), cefotaxime/clavulanic acid (<code>CTC</code>, no ATC code), cefotaxime/sulbactam (<code>CTS</code>, no ATC code), cefotetan (<code>CTT</code>, <a href='https://wLine truncated
<p>The following antibiotics are eligible for the functions <code>eucast_rules()</code> and <code><a href='mdro.html'>mdro()</a></code>. These are shown below in the format 'name (<code>antimicrobial ID</code>, <a href='https://www.whocc.no/atc/structure_and_principles/'>ATC code</a>)', sorted alphabetically:</p>
<p>Amikacin (<code>AMK</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01GB06&amp;showdescription=no'>J01MA02</a>), amoxicillin (<code>AMX</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA04&amp;showdescription=no'>J01MA04</a>), amoxicillin/clavulanic acid (<code>AMC</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CR02&amp;showdescription=no'>J01MA08</a>), ampicillin (<code>AMP</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA01&amp;showdescription=no'>J01MA16</a>), ampicillin/sulbactam (<code>SAM</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CR01&amp;showdescription=no'>J01MA15</a>), azidocillin (<code>AZD</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CE04&amp;showdescription=no'>J01MA11</a>), azithromycin (<code>AZM</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01FA10&amp;showdescription=no'>J01MA12</a>), azlocillin (<code>AZL</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA09&amp;showdescription=no'>J01MA07</a>), aztreonam (<code>ATM</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DF01&amp;showdescription=no'>J01MA14</a>), bacampicillin (<code>BAM</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA06&amp;showdescription=no'>J01MA06</a>), benzathine benzylpenicillin (<code>BNB</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CE08&amp;showdescription=no'>J01MA01</a>), benzathine phenoxymethylpenicillin (<code>BNP</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CE10&amp;showdescription=no'>J01MA18</a>), benzylpenicillin (<code>PEN</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CE01&amp;showdescription=no'>J01MA03</a>), cadazolid (<code>CDZ</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD09&amp;showdescription=no'>J01MA17</a>), carbenicillin (<code>CRB</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA03&amp;showdescription=no'>J01MA10</a>), carindacillin (<code>CRN</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA05&amp;showdescription=no'>J01MA09</a>), cefacetrile (<code>CAC</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB10&amp;showdescription=no'>J01MA05</a>), cefaclor (<code>CEC</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC04&amp;showdescription=no'>J01MA13</a>), cefadroxil (<code>CFR</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB05&amp;showdescription=no'>J01CA01</a>), cefaloridine (<code>RID</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB02&amp;showdescription=no'>J01CA04</a>), cefamandole (<code>MAN</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC03&amp;showdescription=no'>J01CA12</a>), cefatrizine (<code>CTZ</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB07&amp;showdescription=no'>J01CR05</a>), cefazedone (<code>CZD</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB06&amp;showdescription=no'>J01CA13</a>), cefazolin (<code>CZO</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB04&amp;showdescription=no'>J01AA02</a>), cefdinir (<code>CDR</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD15&amp;showdescription=no'>J01FA10</a>), cefditoren (<code>DIT</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD16&amp;showdescription=no'>J01FA09</a>), cefepime (<code>FEP</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DE01&amp;showdescription=no'>J01CR02</a>), cefetamet (<code>CAT</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD10&amp;showdescription=no'>J01AA08</a>), cefixime (<code>CFM</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD08&amp;showdescription=no'>J01FA06</a>), cefmenoxime (<code>CMX</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD05&amp;showdescription=no'>J01CF04</a>), cefmetazole (<code>CMZ</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC09&amp;showdescription=no'>J01CF05</a>), cefodizime (<code>DIZ</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD09&amp;showdescription=no'>J01CR01</a>), cefonicid (<code>CID</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC06&amp;showdescription=no'>J01CE04</a>), cefoperazone (<code>CFP</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD12&amp;showdescription=no'>J01CA09</a>), cefoperazone/sulbactam (<code>CSL</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD62&amp;showdescription=no'>J01DF01</a>), ceforanide (<code>CND</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC11&amp;showdescription=no'>J01CA06</a>), cefotaxime (<code>CTX</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD01&amp;showdescription=no'>J01CE08</a>), cefotetan (<code>CTT</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC05&amp;showdescription=no'>J01CE10</a>), cefotiam (<code>CTF</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC07&amp;showdescription=no'>J01CE0Line truncated
<h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable Lifecycle</h2>
docs/reference/index.html
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@@ -81,7 +81,7 @@
</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">1.6.0.9047</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9048</span>
</span>
</div>
@@ -461,7 +461,7 @@
<tr>
<th colspan="2">
<h2 id="section-analysing-data-antimicrobial-resistance" class="hasAnchor"><a href="#section-analysing-data-antimicrobial-resistance" class="anchor"></a>Analysing data: antimicrobial resistance</h2>
<p class="section-desc"><p>Use these function for the analysis part. You can use <code><a href="../reference/proportion.html">susceptibility()</a></code> or <code><a href="../reference/proportion.html">resistance()</a></code> on any antibiotic column. Be sure to first select the isolates that are appropiate for analysis, by using <code><a href="../reference/first_isolate.html">first_isolate()</a></code> or <code><a href="../reference/get_episode.html">is_new_episode()</a></code>. You can also filter your data on certain resistance in certain antibiotic classes (<code><a href="../reference/filter_ab_class.html">filter_ab_class()</a></code>), or determine multi-drug resistant microorganisms (MDRO, <code><a href="../reference/mdro.html">mdro()</a></code>).</p></p>
<p class="section-desc"><p>Use these function for the analysis part. You can use <code><a href="../reference/proportion.html">susceptibility()</a></code> or <code><a href="../reference/proportion.html">resistance()</a></code> on any antibiotic column. Be sure to first select the isolates that are appropiate for analysis, by using <code><a href="../reference/first_isolate.html">first_isolate()</a></code> or <code><a href="../reference/get_episode.html">is_new_episode()</a></code>. You can also filter your data on certain resistance in certain antibiotic classes (<code><a href="../reference/AMR-deprecated.html">filter_ab_class()</a></code>), or determine multi-drug resistant microorganisms (MDRO, <code><a href="../reference/mdro.html">mdro()</a></code>).</p></p>
</th>
</tr>
@@ -532,9 +532,9 @@
</tr><tr>
<td>
<p><code><a href="filter_ab_class.html">filter_ab_class()</a></code> <code><a href="filter_ab_class.html">filter_aminoglycosides()</a></code> <code><a href="filter_ab_class.html">filter_betalactams()</a></code> <code><a href="filter_ab_class.html">filter_carbapenems()</a></code> <code><a href="filter_ab_class.html">filter_cephalosporins()</a></code> <code><a href="filter_ab_class.html">filter_1st_cephalosporins()</a></code> <code><a href="filter_ab_class.html">filter_2nd_cephalosporins()</a></code> <code><a href="filter_ab_class.html">filter_3rd_cephalosporins()</a></code> <code><a href="filter_ab_class.html">filter_4th_cephalosporins()</a></code> <code><a href="filter_ab_class.html">filter_5th_cephalosporins()</a></code> <code><a href="filter_ab_class.html">filter_fluoroquinolones()</a></code> <code><a href="filter_ab_class.html">filter_glycopeptides()</a></code> <code><a href="filter_ab_class.html">filter_macrolides()</a></code> <code><a href="filter_ab_class.html">filter_oxazolidinones()</a></code> <code><a href="filter_ab_class.html">filter_penicillins()</a></code> <code><a href="filter_ab_class.html">filter_tetracyclines()</a></code> </p>
<p><code><a href="AMR-deprecated.html">p_symbol()</a></code> <code><a href="AMR-deprecated.html">filter_first_weighted_isolate()</a></code> <code><a href="AMR-deprecated.html">key_antibiotics()</a></code> <code><a href="AMR-deprecated.html">key_antibiotics_equal()</a></code> <code><a href="AMR-deprecated.html">filter_ab_class()</a></code> <code><a href="AMR-deprecated.html">filter_aminoglycosides()</a></code> <code><a href="AMR-deprecated.html">filter_betalactams()</a></code> <code><a href="AMR-deprecated.html">filter_carbapenems()</a></code> <code><a href="AMR-deprecated.html">filter_cephalosporins()</a></code> <code><a href="AMR-deprecated.html">filter_1st_cephalosporins()</a></code> <code><a href="AMR-deprecated.html">filter_2nd_cephalosporins()</a></code> <code><a href="AMR-deprecated.html">filter_3rd_cephalosporins()</a></code> <code><a href="AMR-deprecated.html">filter_4th_cephalosporins()</a></code> <code><a href="AMR-deprecated.html">filter_5th_cephalosporins()</a></code> <code><a href="AMR-deprecated.html">filter_fluoroquinolones()</a></code> <code><a href="AMR-deprecated.html">filter_glycopeptides()</a></code> <code><a href="AMR-deprecated.html">filter_macrolides()</a></code> <code><a href="AMR-deprecated.html">filter_oxazolidinones()</a></code> <code><a href="AMR-deprecated.html">filter_penicillins()</a></code> <code><a href="AMR-deprecated.html">filter_tetracyclines()</a></code> </p>
</td>
<td><p>Filter Isolates on Result in Antimicrobial Class</p></td>
<td><p>Deprecated Functions</p></td>
</tr><tr>
<td>
@@ -673,7 +673,7 @@
<tr>
<td>
<p><code><a href="AMR-deprecated.html">p_symbol()</a></code> <code><a href="AMR-deprecated.html">filter_first_weighted_isolate()</a></code> <code><a href="AMR-deprecated.html">key_antibiotics()</a></code> <code><a href="AMR-deprecated.html">key_antibiotics_equal()</a></code> </p>
<p><code><a href="AMR-deprecated.html">p_symbol()</a></code> <code><a href="AMR-deprecated.html">filter_first_weighted_isolate()</a></code> <code><a href="AMR-deprecated.html">key_antibiotics()</a></code> <code><a href="AMR-deprecated.html">key_antibiotics_equal()</a></code> <code><a href="AMR-deprecated.html">filter_ab_class()</a></code> <code><a href="AMR-deprecated.html">filter_aminoglycosides()</a></code> <code><a href="AMR-deprecated.html">filter_betalactams()</a></code> <code><a href="AMR-deprecated.html">filter_carbapenems()</a></code> <code><a href="AMR-deprecated.html">filter_cephalosporins()</a></code> <code><a href="AMR-deprecated.html">filter_1st_cephalosporins()</a></code> <code><a href="AMR-deprecated.html">filter_2nd_cephalosporins()</a></code> <code><a href="AMR-deprecated.html">filter_3rd_cephalosporins()</a></code> <code><a href="AMR-deprecated.html">filter_4th_cephalosporins()</a></code> <code><a href="AMR-deprecated.html">filter_5th_cephalosporins()</a></code> <code><a href="AMR-deprecated.html">filter_fluoroquinolones()</a></code> <code><a href="AMR-deprecated.html">filter_glycopeptides()</a></code> <code><a href="AMR-deprecated.html">filter_macrolides()</a></code> <code><a href="AMR-deprecated.html">filter_oxazolidinones()</a></code> <code><a href="AMR-deprecated.html">filter_penicillins()</a></code> <code><a href="AMR-deprecated.html">filter_tetracyclines()</a></code> </p>
</td>
<td><p>Deprecated Functions</p></td>
</tr>
docs/reference/mdro.html
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</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9044</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9048</span>
</span>
</div>
@@ -402,8 +402,8 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<p>To define antibiotics column names, leave as it is to determine it automatically with <code><a href='guess_ab_col.html'>guess_ab_col()</a></code> or input a text (case-insensitive), or use <code>NULL</code> to skip a column (e.g. <code>TIC = NULL</code> to skip ticarcillin). Manually defined but non-existing columns will be skipped with a warning.</p>
<p>The following antibiotics are used for the functions <code><a href='eucast_rules.html'>eucast_rules()</a></code> and <code>mdro()</code>. These are shown below in the format 'name (<code>antimicrobial ID</code>, <a href='https://www.whocc.no/atc/structure_and_principles/'>ATC code</a>)', sorted alphabetically:</p>
<p>Amikacin (<code>AMK</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01GB06&amp;showdescription=no'>J01GB06</a>), amoxicillin (<code>AMX</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA04&amp;showdescription=no'>J01CA04</a>), amoxicillin/clavulanic acid (<code>AMC</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CR02&amp;showdescription=no'>J01CR02</a>), ampicillin (<code>AMP</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA01&amp;showdescription=no'>J01CA01</a>), ampicillin/sulbactam (<code>SAM</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CR01&amp;showdescription=no'>J01CR01</a>), apalcillin (<code>APL</code>, no ATC code), aspoxicillin (<code>APX</code>, no ATC code), avibactam (<code>AVB</code>, no ATC code), avoparcin (<code>AVO</code>, no ATC code), azidocillin (<code>AZD</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CE04&amp;showdescription=no'>J01CE04</a>), azithromycin (<code>AZM</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01FA10&amp;showdescription=no'>J01FA10</a>), azlocillin (<code>AZL</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA09&amp;showdescription=no'>J01CA09</a>), aztreonam (<code>ATM</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DF01&amp;showdescription=no'>J01DF01</a>), bacampicillin (<code>BAM</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA06&amp;showdescription=no'>J01CA06</a>), benzylpenicillin (<code>PEN</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CE01&amp;showdescription=no'>J01CE01</a>), cadazolid (<code>CDZ</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD09&amp;showdescription=no'>J01DD09</a>), carbenicillin (<code>CRB</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA03&amp;showdescription=no'>J01CA03</a>), carindacillin (<code>CRN</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA05&amp;showdescription=no'>J01CA05</a>), cefacetrile (<code>CAC</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB10&amp;showdescription=no'>J01DB10</a>), cefaclor (<code>CEC</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC04&amp;showdescription=no'>J01DC04</a>), cefadroxil (<code>CFR</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB05&amp;showdescription=no'>J01DB05</a>), cefaloridine (<code>RID</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB02&amp;showdescription=no'>J01DB02</a>), cefamandole (<code>MAN</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC03&amp;showdescription=no'>J01DC03</a>), cefatrizine (<code>CTZ</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB07&amp;showdescription=no'>J01DB07</a>), cefazedone (<code>CZD</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB06&amp;showdescription=no'>J01DB06</a>), cefazolin (<code>CZO</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB04&amp;showdescription=no'>J01DB04</a>), cefcapene (<code>CCP</code>, no ATC code), cefcapene pivoxil (<code>CCX</code>, no ATC code), cefdinir (<code>CDR</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD15&amp;showdescription=no'>J01DD15</a>), cefditoren (<code>DIT</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD16&amp;showdescription=no'>J01DD16</a>), cefditoren pivoxil (<code>DIX</code>, no ATC code), cefepime (<code>FEP</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DE01&amp;showdescription=no'>J01DE01</a>), cefetamet (<code>CAT</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD10&amp;showdescription=no'>J01DD10</a>), cefetamet pivoxil (<code>CPI</code>, no ATC code), cefixime (<code>CFM</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD08&amp;showdescription=no'>J01DD08</a>), cefmenoxime (<code>CMX</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD05&amp;showdescription=no'>J01DD05</a>), cefmetazole (<code>CMZ</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC09&amp;showdescription=no'>J01DC09</a>), cefodizime (<code>DIZ</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD09&amp;showdescription=no'>J01DD09</a>), cefonicid (<code>CID</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC06&amp;showdescription=no'>J01DC06</a>), cefoperazone (<code>CFP</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD12&amp;showdescription=no'>J01DD12</a>), cefoperazone/sulbactam (<code>CSL</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD62&amp;showdescription=no'>J01DD62</a>), ceforanide (<code>CND</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC11&amp;showdescription=no'>J01DC11</a>), cefotaxime (<code>CTX</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD01&amp;showdescription=no'>J01DD01</a>), cefotaxime/clavulanic acid (<code>CTC</code>, no ATC code), cefotaxime/sulbactam (<code>CTS</code>, no ATC code), cefotetan (<code>CTT</code>, <a href='https://wLine truncated
<p>The following antibiotics are eligible for the functions <code><a href='eucast_rules.html'>eucast_rules()</a></code> and <code>mdro()</code>. These are shown below in the format 'name (<code>antimicrobial ID</code>, <a href='https://www.whocc.no/atc/structure_and_principles/'>ATC code</a>)', sorted alphabetically:</p>
<p>Amikacin (<code>AMK</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01GB06&amp;showdescription=no'>J01MA02</a>), amoxicillin (<code>AMX</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA04&amp;showdescription=no'>J01MA04</a>), amoxicillin/clavulanic acid (<code>AMC</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CR02&amp;showdescription=no'>J01MA08</a>), ampicillin (<code>AMP</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA01&amp;showdescription=no'>J01MA16</a>), ampicillin/sulbactam (<code>SAM</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CR01&amp;showdescription=no'>J01MA15</a>), azidocillin (<code>AZD</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CE04&amp;showdescription=no'>J01MA11</a>), azithromycin (<code>AZM</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01FA10&amp;showdescription=no'>J01MA12</a>), azlocillin (<code>AZL</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA09&amp;showdescription=no'>J01MA07</a>), aztreonam (<code>ATM</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DF01&amp;showdescription=no'>J01MA14</a>), bacampicillin (<code>BAM</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA06&amp;showdescription=no'>J01MA06</a>), benzathine benzylpenicillin (<code>BNB</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CE08&amp;showdescription=no'>J01MA01</a>), benzathine phenoxymethylpenicillin (<code>BNP</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CE10&amp;showdescription=no'>J01MA18</a>), benzylpenicillin (<code>PEN</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CE01&amp;showdescription=no'>J01MA03</a>), cadazolid (<code>CDZ</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD09&amp;showdescription=no'>J01MA17</a>), carbenicillin (<code>CRB</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA03&amp;showdescription=no'>J01MA10</a>), carindacillin (<code>CRN</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA05&amp;showdescription=no'>J01MA09</a>), cefacetrile (<code>CAC</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB10&amp;showdescription=no'>J01MA05</a>), cefaclor (<code>CEC</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC04&amp;showdescription=no'>J01MA13</a>), cefadroxil (<code>CFR</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB05&amp;showdescription=no'>J01CA01</a>), cefaloridine (<code>RID</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB02&amp;showdescription=no'>J01CA04</a>), cefamandole (<code>MAN</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC03&amp;showdescription=no'>J01CA12</a>), cefatrizine (<code>CTZ</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB07&amp;showdescription=no'>J01CR05</a>), cefazedone (<code>CZD</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB06&amp;showdescription=no'>J01CA13</a>), cefazolin (<code>CZO</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB04&amp;showdescription=no'>J01AA02</a>), cefdinir (<code>CDR</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD15&amp;showdescription=no'>J01FA10</a>), cefditoren (<code>DIT</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD16&amp;showdescription=no'>J01FA09</a>), cefepime (<code>FEP</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DE01&amp;showdescription=no'>J01CR02</a>), cefetamet (<code>CAT</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD10&amp;showdescription=no'>J01AA08</a>), cefixime (<code>CFM</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD08&amp;showdescription=no'>J01FA06</a>), cefmenoxime (<code>CMX</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD05&amp;showdescription=no'>J01CF04</a>), cefmetazole (<code>CMZ</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC09&amp;showdescription=no'>J01CF05</a>), cefodizime (<code>DIZ</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD09&amp;showdescription=no'>J01CR01</a>), cefonicid (<code>CID</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC06&amp;showdescription=no'>J01CE04</a>), cefoperazone (<code>CFP</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD12&amp;showdescription=no'>J01CA09</a>), cefoperazone/sulbactam (<code>CSL</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD62&amp;showdescription=no'>J01DF01</a>), ceforanide (<code>CND</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC11&amp;showdescription=no'>J01CA06</a>), cefotaxime (<code>CTX</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD01&amp;showdescription=no'>J01CE08</a>), cefotetan (<code>CTT</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC05&amp;showdescription=no'>J01CE10</a>), cefotiam (<code>CTF</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC07&amp;showdescription=no'>J01CE0Line truncated
<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>