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(v1.4.0.9000) more extensive unit tests
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@@ -82,7 +82,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9000</span>
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</span>
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</div>
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@@ -242,33 +242,33 @@
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<p>Use these selection helpers inside any function that allows <a href='https://tidyselect.r-lib.org/reference/language.html'>Tidyverse selection helpers</a>, like <code><a href='https://dplyr.tidyverse.org/reference/select.html'>dplyr::select()</a></code> or <code><a href='https://tidyr.tidyverse.org/reference/pivot_longer.html'>tidyr::pivot_longer()</a></code>. They help to select the columns of antibiotics that are of a specific antibiotic class, without the need to define the columns or antibiotic abbreviations.</p>
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</div>
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<pre class="usage"><span class='fu'>ab_class</span>(<span class='kw'>ab_class</span>)
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<pre class="usage"><span class='fu'>ab_class</span><span class='op'>(</span><span class='va'>ab_class</span><span class='op'>)</span>
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<span class='fu'>aminoglycosides</span>()
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<span class='fu'>aminoglycosides</span><span class='op'>(</span><span class='op'>)</span>
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<span class='fu'>carbapenems</span>()
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<span class='fu'>carbapenems</span><span class='op'>(</span><span class='op'>)</span>
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<span class='fu'>cephalosporins</span>()
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<span class='fu'>cephalosporins</span><span class='op'>(</span><span class='op'>)</span>
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<span class='fu'>cephalosporins_1st</span>()
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<span class='fu'>cephalosporins_1st</span><span class='op'>(</span><span class='op'>)</span>
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<span class='fu'>cephalosporins_2nd</span>()
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<span class='fu'>cephalosporins_2nd</span><span class='op'>(</span><span class='op'>)</span>
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<span class='fu'>cephalosporins_3rd</span>()
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<span class='fu'>cephalosporins_3rd</span><span class='op'>(</span><span class='op'>)</span>
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<span class='fu'>cephalosporins_4th</span>()
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<span class='fu'>cephalosporins_4th</span><span class='op'>(</span><span class='op'>)</span>
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<span class='fu'>cephalosporins_5th</span>()
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<span class='fu'>cephalosporins_5th</span><span class='op'>(</span><span class='op'>)</span>
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<span class='fu'>fluoroquinolones</span>()
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<span class='fu'>fluoroquinolones</span><span class='op'>(</span><span class='op'>)</span>
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<span class='fu'>glycopeptides</span>()
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<span class='fu'>glycopeptides</span><span class='op'>(</span><span class='op'>)</span>
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<span class='fu'>macrolides</span>()
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<span class='fu'>macrolides</span><span class='op'>(</span><span class='op'>)</span>
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<span class='fu'>penicillins</span>()
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<span class='fu'>penicillins</span><span class='op'>(</span><span class='op'>)</span>
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<span class='fu'>tetracyclines</span>()</pre>
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<span class='fu'>tetracyclines</span><span class='op'>(</span><span class='op'>)</span></pre>
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<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
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<table class="ref-arguments">
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@@ -298,34 +298,34 @@
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<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>
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<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
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<pre class="examples"><span class='co'>if</span> (<span class='fu'><a href='https://rdrr.io/r/base/library.html'>require</a></span>(<span class='st'><a href='https://dplyr.tidyverse.org'>"dplyr"</a></span>)) {
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<pre class="examples"><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>
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<span class='co'># this will select columns 'IPM' (imipenem) and 'MEM' (meropenem):</span>
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<span class='kw'>example_isolates</span> <span class='op'>%>%</span>
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<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='fu'>carbapenems</span>())
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<span class='va'>example_isolates</span> <span class='op'>%>%</span>
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<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span><span class='op'>(</span><span class='fu'>carbapenems</span><span class='op'>(</span><span class='op'>)</span><span class='op'>)</span>
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<span class='co'># this will select columns 'mo', 'AMK', 'GEN', 'KAN' and 'TOB':</span>
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<span class='kw'>example_isolates</span> <span class='op'>%>%</span>
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<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='kw'>mo</span>, <span class='fu'>aminoglycosides</span>())
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<span class='va'>example_isolates</span> <span class='op'>%>%</span>
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<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>
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<span class='co'># this will select columns 'mo' and all antimycobacterial drugs ('RIF'):</span>
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<span class='kw'>example_isolates</span> <span class='op'>%>%</span>
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<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='kw'>mo</span>, <span class='fu'>ab_class</span>(<span class='st'>"mycobact"</span>))
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<span class='va'>example_isolates</span> <span class='op'>%>%</span>
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<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>
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<span class='co'># get bug/drug combinations for only macrolides in Gram-positives:</span>
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<span class='kw'>example_isolates</span> <span class='op'>%>%</span>
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<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='fu'><a href='mo_property.html'>mo_gramstain</a></span>(<span class='kw'>mo</span>) <span class='op'>%like%</span> <span class='st'>"pos"</span>) <span class='op'>%>%</span>
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<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='kw'>mo</span>, <span class='fu'>macrolides</span>()) <span class='op'>%>%</span>
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<span class='fu'><a href='bug_drug_combinations.html'>bug_drug_combinations</a></span>() <span class='op'>%>%</span>
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<span class='fu'><a href='https://rdrr.io/r/base/format.html'>format</a></span>()
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<span class='va'>example_isolates</span> <span class='op'>%>%</span>
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<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span><span class='op'>(</span><span class='fu'><a href='mo_property.html'>mo_gramstain</a></span><span class='op'>(</span><span class='va'>mo</span><span class='op'>)</span> <span class='op'>%like%</span> <span class='st'>"pos"</span><span class='op'>)</span> <span class='op'>%>%</span>
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<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'>macrolides</span><span class='op'>(</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>%>%</span>
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<span class='fu'><a href='bug_drug_combinations.html'>bug_drug_combinations</a></span><span class='op'>(</span><span class='op'>)</span> <span class='op'>%>%</span>
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<span class='fu'><a href='https://rdrr.io/r/base/format.html'>format</a></span><span class='op'>(</span><span class='op'>)</span>
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<span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span>(some_column = <span class='st'>"some_value"</span>,
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J01CA01 = <span class='st'>"S"</span>) <span class='op'>%>%</span> <span class='co'># ATC code of ampicillin</span>
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<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='fu'>penicillins</span>()) <span class='co'># only the 'J01CA01' column will be selected</span>
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<span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span><span class='op'>(</span>some_column <span class='op'>=</span> <span class='st'>"some_value"</span>,
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J01CA01 <span class='op'>=</span> <span class='st'>"S"</span><span class='op'>)</span> <span class='op'>%>%</span> <span class='co'># ATC code of ampicillin</span>
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<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>
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}
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<span class='op'>}</span>
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</pre>
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</div>
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<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
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@@ -342,7 +342,7 @@
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</div>
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<div class="pkgdown">
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<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
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<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
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</div>
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</footer>
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