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(v1.4.0.9000) more extensive unit tests
This commit is contained in:
@ -83,7 +83,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
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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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@ -244,39 +244,39 @@ resistance() should be used to calculate resistance, susceptibility() should be
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<p><code>resistance()</code> should be used to calculate resistance, <code>susceptibility()</code> should be used to calculate susceptibility.<br /></p>
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</div>
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<pre class="usage"><span class='fu'>resistance</span>(<span class='kw'>...</span>, minimum = <span class='fl'>30</span>, as_percent = <span class='fl'>FALSE</span>, only_all_tested = <span class='fl'>FALSE</span>)
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<pre class="usage"><span class='fu'>resistance</span><span class='op'>(</span><span class='va'>...</span>, minimum <span class='op'>=</span> <span class='fl'>30</span>, as_percent <span class='op'>=</span> <span class='cn'>FALSE</span>, only_all_tested <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
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<span class='fu'>susceptibility</span>(<span class='kw'>...</span>, minimum = <span class='fl'>30</span>, as_percent = <span class='fl'>FALSE</span>, only_all_tested = <span class='fl'>FALSE</span>)
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<span class='fu'>susceptibility</span><span class='op'>(</span><span class='va'>...</span>, minimum <span class='op'>=</span> <span class='fl'>30</span>, as_percent <span class='op'>=</span> <span class='cn'>FALSE</span>, only_all_tested <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
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<span class='fu'>proportion_R</span>(<span class='kw'>...</span>, minimum = <span class='fl'>30</span>, as_percent = <span class='fl'>FALSE</span>, only_all_tested = <span class='fl'>FALSE</span>)
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<span class='fu'>proportion_R</span><span class='op'>(</span><span class='va'>...</span>, minimum <span class='op'>=</span> <span class='fl'>30</span>, as_percent <span class='op'>=</span> <span class='cn'>FALSE</span>, only_all_tested <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
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<span class='fu'>proportion_IR</span>(<span class='kw'>...</span>, minimum = <span class='fl'>30</span>, as_percent = <span class='fl'>FALSE</span>, only_all_tested = <span class='fl'>FALSE</span>)
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<span class='fu'>proportion_IR</span><span class='op'>(</span><span class='va'>...</span>, minimum <span class='op'>=</span> <span class='fl'>30</span>, as_percent <span class='op'>=</span> <span class='cn'>FALSE</span>, only_all_tested <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
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<span class='fu'>proportion_I</span>(<span class='kw'>...</span>, minimum = <span class='fl'>30</span>, as_percent = <span class='fl'>FALSE</span>, only_all_tested = <span class='fl'>FALSE</span>)
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<span class='fu'>proportion_I</span><span class='op'>(</span><span class='va'>...</span>, minimum <span class='op'>=</span> <span class='fl'>30</span>, as_percent <span class='op'>=</span> <span class='cn'>FALSE</span>, only_all_tested <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
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<span class='fu'>proportion_SI</span>(<span class='kw'>...</span>, minimum = <span class='fl'>30</span>, as_percent = <span class='fl'>FALSE</span>, only_all_tested = <span class='fl'>FALSE</span>)
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<span class='fu'>proportion_SI</span><span class='op'>(</span><span class='va'>...</span>, minimum <span class='op'>=</span> <span class='fl'>30</span>, as_percent <span class='op'>=</span> <span class='cn'>FALSE</span>, only_all_tested <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
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<span class='fu'>proportion_S</span>(<span class='kw'>...</span>, minimum = <span class='fl'>30</span>, as_percent = <span class='fl'>FALSE</span>, only_all_tested = <span class='fl'>FALSE</span>)
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<span class='fu'>proportion_S</span><span class='op'>(</span><span class='va'>...</span>, minimum <span class='op'>=</span> <span class='fl'>30</span>, as_percent <span class='op'>=</span> <span class='cn'>FALSE</span>, only_all_tested <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
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<span class='fu'>proportion_df</span>(
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<span class='kw'>data</span>,
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translate_ab = <span class='st'>"name"</span>,
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language = <span class='fu'><a href='translate.html'>get_locale</a></span>(),
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minimum = <span class='fl'>30</span>,
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as_percent = <span class='fl'>FALSE</span>,
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combine_SI = <span class='fl'>TRUE</span>,
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combine_IR = <span class='fl'>FALSE</span>
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)
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<span class='fu'>proportion_df</span><span class='op'>(</span>
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<span class='va'>data</span>,
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translate_ab <span class='op'>=</span> <span class='st'>"name"</span>,
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language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>,
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minimum <span class='op'>=</span> <span class='fl'>30</span>,
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as_percent <span class='op'>=</span> <span class='cn'>FALSE</span>,
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combine_SI <span class='op'>=</span> <span class='cn'>TRUE</span>,
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combine_IR <span class='op'>=</span> <span class='cn'>FALSE</span>
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<span class='op'>)</span>
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<span class='fu'>rsi_df</span>(
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<span class='kw'>data</span>,
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translate_ab = <span class='st'>"name"</span>,
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language = <span class='fu'><a href='translate.html'>get_locale</a></span>(),
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minimum = <span class='fl'>30</span>,
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as_percent = <span class='fl'>FALSE</span>,
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combine_SI = <span class='fl'>TRUE</span>,
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combine_IR = <span class='fl'>FALSE</span>
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)</pre>
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<span class='fu'>rsi_df</span><span class='op'>(</span>
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<span class='va'>data</span>,
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translate_ab <span class='op'>=</span> <span class='st'>"name"</span>,
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language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>,
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minimum <span class='op'>=</span> <span class='fl'>30</span>,
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as_percent <span class='op'>=</span> <span class='cn'>FALSE</span>,
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combine_SI <span class='op'>=</span> <span class='cn'>TRUE</span>,
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combine_IR <span class='op'>=</span> <span class='cn'>FALSE</span>
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<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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@ -353,12 +353,12 @@ resistance() should be used to calculate resistance, susceptibility() should be
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--------------------------------------------------------------------
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</pre>
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<p>Please note that, in combination therapies, for <code>only_all_tested = TRUE</code> applies that:</p><pre> <span class='fu'><a href='count.html'>count_S</a></span>() <span class='op'>+</span> <span class='fu'><a href='count.html'>count_I</a></span>() <span class='op'>+</span> <span class='fu'><a href='count.html'>count_R</a></span>() <span class='op'>=</span> <span class='fu'><a href='count.html'>count_all</a></span>()
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<span class='fu'>proportion_S</span>() <span class='op'>+</span> <span class='fu'>proportion_I</span>() <span class='op'>+</span> <span class='fu'>proportion_R</span>() <span class='op'>=</span> <span class='fl'>1</span>
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<p>Please note that, in combination therapies, for <code>only_all_tested = TRUE</code> applies that:</p><pre> <span class='fu'><a href='count.html'>count_S</a></span><span class='op'>(</span><span class='op'>)</span> <span class='op'>+</span> <span class='fu'><a href='count.html'>count_I</a></span><span class='op'>(</span><span class='op'>)</span> <span class='op'>+</span> <span class='fu'><a href='count.html'>count_R</a></span><span class='op'>(</span><span class='op'>)</span> <span class='op'>=</span> <span class='fu'><a href='count.html'>count_all</a></span><span class='op'>(</span><span class='op'>)</span>
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<span class='fu'>proportion_S</span><span class='op'>(</span><span class='op'>)</span> <span class='op'>+</span> <span class='fu'>proportion_I</span><span class='op'>(</span><span class='op'>)</span> <span class='op'>+</span> <span class='fu'>proportion_R</span><span class='op'>(</span><span class='op'>)</span> <span class='op'>=</span> <span class='fl'>1</span>
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</pre>
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<p>and that, in combination therapies, for <code>only_all_tested = FALSE</code> applies that:</p><pre> <span class='fu'><a href='count.html'>count_S</a></span>() <span class='op'>+</span> <span class='fu'><a href='count.html'>count_I</a></span>() <span class='op'>+</span> <span class='fu'><a href='count.html'>count_R</a></span>() <span class='op'>>=</span> <span class='fu'><a href='count.html'>count_all</a></span>()
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<span class='fu'>proportion_S</span>() <span class='op'>+</span> <span class='fu'>proportion_I</span>() <span class='op'>+</span> <span class='fu'>proportion_R</span>() <span class='op'>>=</span> <span class='fl'>1</span>
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<p>and that, in combination therapies, for <code>only_all_tested = FALSE</code> applies that:</p><pre> <span class='fu'><a href='count.html'>count_S</a></span><span class='op'>(</span><span class='op'>)</span> <span class='op'>+</span> <span class='fu'><a href='count.html'>count_I</a></span><span class='op'>(</span><span class='op'>)</span> <span class='op'>+</span> <span class='fu'><a href='count.html'>count_R</a></span><span class='op'>(</span><span class='op'>)</span> <span class='op'>>=</span> <span class='fu'><a href='count.html'>count_all</a></span><span class='op'>(</span><span class='op'>)</span>
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<span class='fu'>proportion_S</span><span class='op'>(</span><span class='op'>)</span> <span class='op'>+</span> <span class='fu'>proportion_I</span><span class='op'>(</span><span class='op'>)</span> <span class='op'>+</span> <span class='fu'>proportion_R</span><span class='op'>(</span><span class='op'>)</span> <span class='op'>>=</span> <span class='fl'>1</span>
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</pre>
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<p>Using <code>only_all_tested</code> has no impact when only using one antibiotic as input.</p>
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@ -394,76 +394,76 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
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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'># example_isolates is a data set available in the AMR package.</span>
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<span class='op'>?</span><span class='kw'>example_isolates</span>
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<span class='op'>?</span><span class='va'>example_isolates</span>
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<span class='fu'>resistance</span>(<span class='kw'>example_isolates</span><span class='op'>$</span><span class='kw'>AMX</span>) <span class='co'># determines %R</span>
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<span class='fu'>susceptibility</span>(<span class='kw'>example_isolates</span><span class='op'>$</span><span class='kw'>AMX</span>) <span class='co'># determines %S+I</span>
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<span class='fu'>resistance</span><span class='op'>(</span><span class='va'>example_isolates</span><span class='op'>$</span><span class='va'>AMX</span><span class='op'>)</span> <span class='co'># determines %R</span>
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<span class='fu'>susceptibility</span><span class='op'>(</span><span class='va'>example_isolates</span><span class='op'>$</span><span class='va'>AMX</span><span class='op'>)</span> <span class='co'># determines %S+I</span>
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<span class='co'># be more specific</span>
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<span class='fu'>proportion_S</span>(<span class='kw'>example_isolates</span><span class='op'>$</span><span class='kw'>AMX</span>)
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<span class='fu'>proportion_SI</span>(<span class='kw'>example_isolates</span><span class='op'>$</span><span class='kw'>AMX</span>)
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<span class='fu'>proportion_I</span>(<span class='kw'>example_isolates</span><span class='op'>$</span><span class='kw'>AMX</span>)
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<span class='fu'>proportion_IR</span>(<span class='kw'>example_isolates</span><span class='op'>$</span><span class='kw'>AMX</span>)
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<span class='fu'>proportion_R</span>(<span class='kw'>example_isolates</span><span class='op'>$</span><span class='kw'>AMX</span>)
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<span class='fu'>proportion_S</span><span class='op'>(</span><span class='va'>example_isolates</span><span class='op'>$</span><span class='va'>AMX</span><span class='op'>)</span>
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<span class='fu'>proportion_SI</span><span class='op'>(</span><span class='va'>example_isolates</span><span class='op'>$</span><span class='va'>AMX</span><span class='op'>)</span>
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<span class='fu'>proportion_I</span><span class='op'>(</span><span class='va'>example_isolates</span><span class='op'>$</span><span class='va'>AMX</span><span class='op'>)</span>
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<span class='fu'>proportion_IR</span><span class='op'>(</span><span class='va'>example_isolates</span><span class='op'>$</span><span class='va'>AMX</span><span class='op'>)</span>
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<span class='fu'>proportion_R</span><span class='op'>(</span><span class='va'>example_isolates</span><span class='op'>$</span><span class='va'>AMX</span><span class='op'>)</span>
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<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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<span class='kw'>example_isolates</span> <span class='op'>%>%</span>
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<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='kw'>hospital_id</span>) <span class='op'>%>%</span>
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<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(r = <span class='fu'>resistance</span>(<span class='kw'>CIP</span>),
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n = <span class='fu'><a href='count.html'>n_rsi</a></span>(<span class='kw'>CIP</span>)) <span class='co'># n_rsi works like n_distinct in dplyr, see ?n_rsi</span>
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<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='va'>example_isolates</span> <span class='op'>%>%</span>
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<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span><span class='op'>(</span><span class='va'>hospital_id</span><span class='op'>)</span> <span class='op'>%>%</span>
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<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span><span class='op'>(</span>r <span class='op'>=</span> <span class='fu'>resistance</span><span class='op'>(</span><span class='va'>CIP</span><span class='op'>)</span>,
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n <span class='op'>=</span> <span class='fu'><a href='count.html'>n_rsi</a></span><span class='op'>(</span><span class='va'>CIP</span><span class='op'>)</span><span class='op'>)</span> <span class='co'># n_rsi works like n_distinct in dplyr, see ?n_rsi</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/group_by.html'>group_by</a></span>(<span class='kw'>hospital_id</span>) <span class='op'>%>%</span>
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<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(R = <span class='fu'>resistance</span>(<span class='kw'>CIP</span>, as_percent = <span class='fl'>TRUE</span>),
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SI = <span class='fu'>susceptibility</span>(<span class='kw'>CIP</span>, as_percent = <span class='fl'>TRUE</span>),
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n1 = <span class='fu'><a href='count.html'>count_all</a></span>(<span class='kw'>CIP</span>), <span class='co'># the actual total; sum of all three</span>
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n2 = <span class='fu'><a href='count.html'>n_rsi</a></span>(<span class='kw'>CIP</span>), <span class='co'># same - analogous to n_distinct</span>
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total = <span class='fu'><a href='https://dplyr.tidyverse.org/reference/context.html'>n</a></span>()) <span class='co'># NOT the number of tested isolates!</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/group_by.html'>group_by</a></span><span class='op'>(</span><span class='va'>hospital_id</span><span class='op'>)</span> <span class='op'>%>%</span>
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<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span><span class='op'>(</span>R <span class='op'>=</span> <span class='fu'>resistance</span><span class='op'>(</span><span class='va'>CIP</span>, as_percent <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>,
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SI <span class='op'>=</span> <span class='fu'>susceptibility</span><span class='op'>(</span><span class='va'>CIP</span>, as_percent <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>,
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n1 <span class='op'>=</span> <span class='fu'><a href='count.html'>count_all</a></span><span class='op'>(</span><span class='va'>CIP</span><span class='op'>)</span>, <span class='co'># the actual total; sum of all three</span>
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n2 <span class='op'>=</span> <span class='fu'><a href='count.html'>n_rsi</a></span><span class='op'>(</span><span class='va'>CIP</span><span class='op'>)</span>, <span class='co'># same - analogous to n_distinct</span>
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total <span class='op'>=</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/context.html'>n</a></span><span class='op'>(</span><span class='op'>)</span><span class='op'>)</span> <span class='co'># NOT the number of tested isolates!</span>
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<span class='co'># Calculate co-resistance between amoxicillin/clav acid and gentamicin,</span>
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<span class='co'># so we can see that combination therapy does a lot more than mono therapy:</span>
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<span class='kw'>example_isolates</span> <span class='op'>%>%</span> <span class='fu'>susceptibility</span>(<span class='kw'>AMC</span>) <span class='co'># %SI = 76.3%</span>
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<span class='kw'>example_isolates</span> <span class='op'>%>%</span> <span class='fu'><a href='count.html'>count_all</a></span>(<span class='kw'>AMC</span>) <span class='co'># n = 1879</span>
|
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<span class='va'>example_isolates</span> <span class='op'>%>%</span> <span class='fu'>susceptibility</span><span class='op'>(</span><span class='va'>AMC</span><span class='op'>)</span> <span class='co'># %SI = 76.3%</span>
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<span class='va'>example_isolates</span> <span class='op'>%>%</span> <span class='fu'><a href='count.html'>count_all</a></span><span class='op'>(</span><span class='va'>AMC</span><span class='op'>)</span> <span class='co'># n = 1879</span>
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<span class='kw'>example_isolates</span> <span class='op'>%>%</span> <span class='fu'>susceptibility</span>(<span class='kw'>GEN</span>) <span class='co'># %SI = 75.4%</span>
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<span class='kw'>example_isolates</span> <span class='op'>%>%</span> <span class='fu'><a href='count.html'>count_all</a></span>(<span class='kw'>GEN</span>) <span class='co'># n = 1855</span>
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<span class='va'>example_isolates</span> <span class='op'>%>%</span> <span class='fu'>susceptibility</span><span class='op'>(</span><span class='va'>GEN</span><span class='op'>)</span> <span class='co'># %SI = 75.4%</span>
|
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<span class='va'>example_isolates</span> <span class='op'>%>%</span> <span class='fu'><a href='count.html'>count_all</a></span><span class='op'>(</span><span class='va'>GEN</span><span class='op'>)</span> <span class='co'># n = 1855</span>
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<span class='kw'>example_isolates</span> <span class='op'>%>%</span> <span class='fu'>susceptibility</span>(<span class='kw'>AMC</span>, <span class='kw'>GEN</span>) <span class='co'># %SI = 94.1%</span>
|
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<span class='kw'>example_isolates</span> <span class='op'>%>%</span> <span class='fu'><a href='count.html'>count_all</a></span>(<span class='kw'>AMC</span>, <span class='kw'>GEN</span>) <span class='co'># n = 1939</span>
|
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<span class='va'>example_isolates</span> <span class='op'>%>%</span> <span class='fu'>susceptibility</span><span class='op'>(</span><span class='va'>AMC</span>, <span class='va'>GEN</span><span class='op'>)</span> <span class='co'># %SI = 94.1%</span>
|
||||
<span class='va'>example_isolates</span> <span class='op'>%>%</span> <span class='fu'><a href='count.html'>count_all</a></span><span class='op'>(</span><span class='va'>AMC</span>, <span class='va'>GEN</span><span class='op'>)</span> <span class='co'># n = 1939</span>
|
||||
|
||||
|
||||
<span class='co'># See Details on how `only_all_tested` works. Example:</span>
|
||||
<span class='kw'>example_isolates</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(numerator = <span class='fu'><a href='count.html'>count_susceptible</a></span>(<span class='kw'>AMC</span>, <span class='kw'>GEN</span>),
|
||||
denominator = <span class='fu'><a href='count.html'>count_all</a></span>(<span class='kw'>AMC</span>, <span class='kw'>GEN</span>),
|
||||
proportion = <span class='fu'>susceptibility</span>(<span class='kw'>AMC</span>, <span class='kw'>GEN</span>))
|
||||
<span class='va'>example_isolates</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span><span class='op'>(</span>numerator <span class='op'>=</span> <span class='fu'><a href='count.html'>count_susceptible</a></span><span class='op'>(</span><span class='va'>AMC</span>, <span class='va'>GEN</span><span class='op'>)</span>,
|
||||
denominator <span class='op'>=</span> <span class='fu'><a href='count.html'>count_all</a></span><span class='op'>(</span><span class='va'>AMC</span>, <span class='va'>GEN</span><span class='op'>)</span>,
|
||||
proportion <span class='op'>=</span> <span class='fu'>susceptibility</span><span class='op'>(</span><span class='va'>AMC</span>, <span class='va'>GEN</span><span class='op'>)</span><span class='op'>)</span>
|
||||
|
||||
<span class='kw'>example_isolates</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(numerator = <span class='fu'><a href='count.html'>count_susceptible</a></span>(<span class='kw'>AMC</span>, <span class='kw'>GEN</span>, only_all_tested = <span class='fl'>TRUE</span>),
|
||||
denominator = <span class='fu'><a href='count.html'>count_all</a></span>(<span class='kw'>AMC</span>, <span class='kw'>GEN</span>, only_all_tested = <span class='fl'>TRUE</span>),
|
||||
proportion = <span class='fu'>susceptibility</span>(<span class='kw'>AMC</span>, <span class='kw'>GEN</span>, only_all_tested = <span class='fl'>TRUE</span>))
|
||||
<span class='va'>example_isolates</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span><span class='op'>(</span>numerator <span class='op'>=</span> <span class='fu'><a href='count.html'>count_susceptible</a></span><span class='op'>(</span><span class='va'>AMC</span>, <span class='va'>GEN</span>, only_all_tested <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>,
|
||||
denominator <span class='op'>=</span> <span class='fu'><a href='count.html'>count_all</a></span><span class='op'>(</span><span class='va'>AMC</span>, <span class='va'>GEN</span>, only_all_tested <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>,
|
||||
proportion <span class='op'>=</span> <span class='fu'>susceptibility</span><span class='op'>(</span><span class='va'>AMC</span>, <span class='va'>GEN</span>, only_all_tested <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span><span class='op'>)</span>
|
||||
|
||||
|
||||
<span class='kw'>example_isolates</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='kw'>hospital_id</span>) <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(cipro_p = <span class='fu'>susceptibility</span>(<span class='kw'>CIP</span>, as_percent = <span class='fl'>TRUE</span>),
|
||||
cipro_n = <span class='fu'><a href='count.html'>count_all</a></span>(<span class='kw'>CIP</span>),
|
||||
genta_p = <span class='fu'>susceptibility</span>(<span class='kw'>GEN</span>, as_percent = <span class='fl'>TRUE</span>),
|
||||
genta_n = <span class='fu'><a href='count.html'>count_all</a></span>(<span class='kw'>GEN</span>),
|
||||
combination_p = <span class='fu'>susceptibility</span>(<span class='kw'>CIP</span>, <span class='kw'>GEN</span>, as_percent = <span class='fl'>TRUE</span>),
|
||||
combination_n = <span class='fu'><a href='count.html'>count_all</a></span>(<span class='kw'>CIP</span>, <span class='kw'>GEN</span>))
|
||||
<span class='va'>example_isolates</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span><span class='op'>(</span><span class='va'>hospital_id</span><span class='op'>)</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span><span class='op'>(</span>cipro_p <span class='op'>=</span> <span class='fu'>susceptibility</span><span class='op'>(</span><span class='va'>CIP</span>, as_percent <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>,
|
||||
cipro_n <span class='op'>=</span> <span class='fu'><a href='count.html'>count_all</a></span><span class='op'>(</span><span class='va'>CIP</span><span class='op'>)</span>,
|
||||
genta_p <span class='op'>=</span> <span class='fu'>susceptibility</span><span class='op'>(</span><span class='va'>GEN</span>, as_percent <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>,
|
||||
genta_n <span class='op'>=</span> <span class='fu'><a href='count.html'>count_all</a></span><span class='op'>(</span><span class='va'>GEN</span><span class='op'>)</span>,
|
||||
combination_p <span class='op'>=</span> <span class='fu'>susceptibility</span><span class='op'>(</span><span class='va'>CIP</span>, <span class='va'>GEN</span>, as_percent <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>,
|
||||
combination_n <span class='op'>=</span> <span class='fu'><a href='count.html'>count_all</a></span><span class='op'>(</span><span class='va'>CIP</span>, <span class='va'>GEN</span><span class='op'>)</span><span class='op'>)</span>
|
||||
|
||||
<span class='co'># Get proportions S/I/R immediately of all rsi columns</span>
|
||||
<span class='kw'>example_isolates</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='kw'>AMX</span>, <span class='kw'>CIP</span>) <span class='op'>%>%</span>
|
||||
<span class='fu'>proportion_df</span>(translate = <span class='fl'>FALSE</span>)
|
||||
<span class='va'>example_isolates</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span><span class='op'>(</span><span class='va'>AMX</span>, <span class='va'>CIP</span><span class='op'>)</span> <span class='op'>%>%</span>
|
||||
<span class='fu'>proportion_df</span><span class='op'>(</span>translate <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
|
||||
|
||||
<span class='co'># It also supports grouping variables</span>
|
||||
<span class='kw'>example_isolates</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='kw'>hospital_id</span>, <span class='kw'>AMX</span>, <span class='kw'>CIP</span>) <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='kw'>hospital_id</span>) <span class='op'>%>%</span>
|
||||
<span class='fu'>proportion_df</span>(translate = <span class='fl'>FALSE</span>)
|
||||
}
|
||||
<span class='va'>example_isolates</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span><span class='op'>(</span><span class='va'>hospital_id</span>, <span class='va'>AMX</span>, <span class='va'>CIP</span><span class='op'>)</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span><span class='op'>(</span><span class='va'>hospital_id</span><span class='op'>)</span> <span class='op'>%>%</span>
|
||||
<span class='fu'>proportion_df</span><span class='op'>(</span>translate <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
|
||||
<span class='op'>}</span>
|
||||
</pre>
|
||||
</div>
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
|
||||
@ -480,7 +480,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
Reference in New Issue
Block a user