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(v1.4.0.9000) more extensive unit tests
This commit is contained in:
@ -83,7 +83,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
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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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@ -244,31 +244,31 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
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<p><code>count_resistant()</code> should be used to count resistant isolates, <code>count_susceptible()</code> should be used to count susceptible isolates.</p>
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</div>
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<pre class="usage"><span class='fu'>count_resistant</span>(<span class='kw'>...</span>, only_all_tested = <span class='fl'>FALSE</span>)
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<pre class="usage"><span class='fu'>count_resistant</span><span class='op'>(</span><span class='va'>...</span>, only_all_tested <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
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<span class='fu'>count_susceptible</span>(<span class='kw'>...</span>, only_all_tested = <span class='fl'>FALSE</span>)
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<span class='fu'>count_susceptible</span><span class='op'>(</span><span class='va'>...</span>, only_all_tested <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
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<span class='fu'>count_R</span>(<span class='kw'>...</span>, only_all_tested = <span class='fl'>FALSE</span>)
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<span class='fu'>count_R</span><span class='op'>(</span><span class='va'>...</span>, only_all_tested <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
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<span class='fu'>count_IR</span>(<span class='kw'>...</span>, only_all_tested = <span class='fl'>FALSE</span>)
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<span class='fu'>count_IR</span><span class='op'>(</span><span class='va'>...</span>, only_all_tested <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
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<span class='fu'>count_I</span>(<span class='kw'>...</span>, only_all_tested = <span class='fl'>FALSE</span>)
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<span class='fu'>count_I</span><span class='op'>(</span><span class='va'>...</span>, only_all_tested <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
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<span class='fu'>count_SI</span>(<span class='kw'>...</span>, only_all_tested = <span class='fl'>FALSE</span>)
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<span class='fu'>count_SI</span><span class='op'>(</span><span class='va'>...</span>, only_all_tested <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
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<span class='fu'>count_S</span>(<span class='kw'>...</span>, only_all_tested = <span class='fl'>FALSE</span>)
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<span class='fu'>count_S</span><span class='op'>(</span><span class='va'>...</span>, only_all_tested <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
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<span class='fu'>count_all</span>(<span class='kw'>...</span>, only_all_tested = <span class='fl'>FALSE</span>)
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<span class='fu'>count_all</span><span class='op'>(</span><span class='va'>...</span>, only_all_tested <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
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<span class='fu'>n_rsi</span>(<span class='kw'>...</span>, only_all_tested = <span class='fl'>FALSE</span>)
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<span class='fu'>n_rsi</span><span class='op'>(</span><span class='va'>...</span>, only_all_tested <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
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<span class='fu'>count_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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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'>count_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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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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@ -355,12 +355,12 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
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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'>count_S</span>() <span class='op'>+</span> <span class='fu'>count_I</span>() <span class='op'>+</span> <span class='fu'>count_R</span>() <span class='op'>=</span> <span class='fu'>count_all</span>()
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<span class='fu'><a href='proportion.html'>proportion_S</a></span>() <span class='op'>+</span> <span class='fu'><a href='proportion.html'>proportion_I</a></span>() <span class='op'>+</span> <span class='fu'><a href='proportion.html'>proportion_R</a></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'>count_S</span><span class='op'>(</span><span class='op'>)</span> <span class='op'>+</span> <span class='fu'>count_I</span><span class='op'>(</span><span class='op'>)</span> <span class='op'>+</span> <span class='fu'>count_R</span><span class='op'>(</span><span class='op'>)</span> <span class='op'>=</span> <span class='fu'>count_all</span><span class='op'>(</span><span class='op'>)</span>
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<span class='fu'><a href='proportion.html'>proportion_S</a></span><span class='op'>(</span><span class='op'>)</span> <span class='op'>+</span> <span class='fu'><a href='proportion.html'>proportion_I</a></span><span class='op'>(</span><span class='op'>)</span> <span class='op'>+</span> <span class='fu'><a href='proportion.html'>proportion_R</a></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'>count_S</span>() <span class='op'>+</span> <span class='fu'>count_I</span>() <span class='op'>+</span> <span class='fu'>count_R</span>() <span class='op'>>=</span> <span class='fu'>count_all</span>()
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<span class='fu'><a href='proportion.html'>proportion_S</a></span>() <span class='op'>+</span> <span class='fu'><a href='proportion.html'>proportion_I</a></span>() <span class='op'>+</span> <span class='fu'><a href='proportion.html'>proportion_R</a></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'>count_S</span><span class='op'>(</span><span class='op'>)</span> <span class='op'>+</span> <span class='fu'>count_I</span><span class='op'>(</span><span class='op'>)</span> <span class='op'>+</span> <span class='fu'>count_R</span><span class='op'>(</span><span class='op'>)</span> <span class='op'>>=</span> <span class='fu'>count_all</span><span class='op'>(</span><span class='op'>)</span>
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<span class='fu'><a href='proportion.html'>proportion_S</a></span><span class='op'>(</span><span class='op'>)</span> <span class='op'>+</span> <span class='fu'><a href='proportion.html'>proportion_I</a></span><span class='op'>(</span><span class='op'>)</span> <span class='op'>+</span> <span class='fu'><a href='proportion.html'>proportion_R</a></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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@ -375,64 +375,64 @@ 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'>count_resistant</span>(<span class='kw'>example_isolates</span><span class='op'>$</span><span class='kw'>AMX</span>) <span class='co'># counts "R"</span>
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<span class='fu'>count_susceptible</span>(<span class='kw'>example_isolates</span><span class='op'>$</span><span class='kw'>AMX</span>) <span class='co'># counts "S" and "I"</span>
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<span class='fu'>count_all</span>(<span class='kw'>example_isolates</span><span class='op'>$</span><span class='kw'>AMX</span>) <span class='co'># counts "S", "I" and "R"</span>
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<span class='fu'>count_resistant</span><span class='op'>(</span><span class='va'>example_isolates</span><span class='op'>$</span><span class='va'>AMX</span><span class='op'>)</span> <span class='co'># counts "R"</span>
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<span class='fu'>count_susceptible</span><span class='op'>(</span><span class='va'>example_isolates</span><span class='op'>$</span><span class='va'>AMX</span><span class='op'>)</span> <span class='co'># counts "S" and "I"</span>
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<span class='fu'>count_all</span><span class='op'>(</span><span class='va'>example_isolates</span><span class='op'>$</span><span class='va'>AMX</span><span class='op'>)</span> <span class='co'># counts "S", "I" and "R"</span>
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<span class='co'># be more specific</span>
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<span class='fu'>count_S</span>(<span class='kw'>example_isolates</span><span class='op'>$</span><span class='kw'>AMX</span>)
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<span class='fu'>count_SI</span>(<span class='kw'>example_isolates</span><span class='op'>$</span><span class='kw'>AMX</span>)
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<span class='fu'>count_I</span>(<span class='kw'>example_isolates</span><span class='op'>$</span><span class='kw'>AMX</span>)
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<span class='fu'>count_IR</span>(<span class='kw'>example_isolates</span><span class='op'>$</span><span class='kw'>AMX</span>)
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<span class='fu'>count_R</span>(<span class='kw'>example_isolates</span><span class='op'>$</span><span class='kw'>AMX</span>)
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<span class='fu'>count_S</span><span class='op'>(</span><span class='va'>example_isolates</span><span class='op'>$</span><span class='va'>AMX</span><span class='op'>)</span>
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<span class='fu'>count_SI</span><span class='op'>(</span><span class='va'>example_isolates</span><span class='op'>$</span><span class='va'>AMX</span><span class='op'>)</span>
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<span class='fu'>count_I</span><span class='op'>(</span><span class='va'>example_isolates</span><span class='op'>$</span><span class='va'>AMX</span><span class='op'>)</span>
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<span class='fu'>count_IR</span><span class='op'>(</span><span class='va'>example_isolates</span><span class='op'>$</span><span class='va'>AMX</span><span class='op'>)</span>
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<span class='fu'>count_R</span><span class='op'>(</span><span class='va'>example_isolates</span><span class='op'>$</span><span class='va'>AMX</span><span class='op'>)</span>
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<span class='co'># Count all available isolates</span>
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<span class='fu'>count_all</span>(<span class='kw'>example_isolates</span><span class='op'>$</span><span class='kw'>AMX</span>)
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<span class='fu'>n_rsi</span>(<span class='kw'>example_isolates</span><span class='op'>$</span><span class='kw'>AMX</span>)
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<span class='fu'>count_all</span><span class='op'>(</span><span class='va'>example_isolates</span><span class='op'>$</span><span class='va'>AMX</span><span class='op'>)</span>
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<span class='fu'>n_rsi</span><span class='op'>(</span><span class='va'>example_isolates</span><span class='op'>$</span><span class='va'>AMX</span><span class='op'>)</span>
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<span class='co'># n_rsi() is an alias of count_all().</span>
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<span class='co'># Since it counts all available isolates, you can</span>
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<span class='co'># calculate back to count e.g. susceptible isolates.</span>
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<span class='co'># These results are the same:</span>
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<span class='fu'>count_susceptible</span>(<span class='kw'>example_isolates</span><span class='op'>$</span><span class='kw'>AMX</span>)
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<span class='fu'><a href='proportion.html'>susceptibility</a></span>(<span class='kw'>example_isolates</span><span class='op'>$</span><span class='kw'>AMX</span>) <span class='op'>*</span> <span class='fu'>n_rsi</span>(<span class='kw'>example_isolates</span><span class='op'>$</span><span class='kw'>AMX</span>)
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<span class='fu'>count_susceptible</span><span class='op'>(</span><span class='va'>example_isolates</span><span class='op'>$</span><span class='va'>AMX</span><span class='op'>)</span>
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<span class='fu'><a href='proportion.html'>susceptibility</a></span><span class='op'>(</span><span class='va'>example_isolates</span><span class='op'>$</span><span class='va'>AMX</span><span class='op'>)</span> <span class='op'>*</span> <span class='fu'>n_rsi</span><span class='op'>(</span><span class='va'>example_isolates</span><span class='op'>$</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'>count_R</span>(<span class='kw'>CIP</span>),
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I = <span class='fu'>count_I</span>(<span class='kw'>CIP</span>),
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S = <span class='fu'>count_S</span>(<span class='kw'>CIP</span>),
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n1 = <span class='fu'>count_all</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'>n_rsi</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='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'>count_R</span><span class='op'>(</span><span class='va'>CIP</span><span class='op'>)</span>,
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I <span class='op'>=</span> <span class='fu'>count_I</span><span class='op'>(</span><span class='va'>CIP</span><span class='op'>)</span>,
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S <span class='op'>=</span> <span class='fu'>count_S</span><span class='op'>(</span><span class='va'>CIP</span><span class='op'>)</span>,
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n1 <span class='op'>=</span> <span class='fu'>count_all</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'>n_rsi</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'># Count 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='co'># Please mind that `susceptibility()` calculates percentages right away instead.</span>
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<span class='kw'>example_isolates</span> <span class='op'>%>%</span> <span class='fu'>count_susceptible</span>(<span class='kw'>AMC</span>) <span class='co'># 1433</span>
|
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<span class='kw'>example_isolates</span> <span class='op'>%>%</span> <span class='fu'>count_all</span>(<span class='kw'>AMC</span>) <span class='co'># 1879</span>
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<span class='va'>example_isolates</span> <span class='op'>%>%</span> <span class='fu'>count_susceptible</span><span class='op'>(</span><span class='va'>AMC</span><span class='op'>)</span> <span class='co'># 1433</span>
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<span class='va'>example_isolates</span> <span class='op'>%>%</span> <span class='fu'>count_all</span><span class='op'>(</span><span class='va'>AMC</span><span class='op'>)</span> <span class='co'># 1879</span>
|
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<span class='kw'>example_isolates</span> <span class='op'>%>%</span> <span class='fu'>count_susceptible</span>(<span class='kw'>GEN</span>) <span class='co'># 1399</span>
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<span class='kw'>example_isolates</span> <span class='op'>%>%</span> <span class='fu'>count_all</span>(<span class='kw'>GEN</span>) <span class='co'># 1855</span>
|
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<span class='va'>example_isolates</span> <span class='op'>%>%</span> <span class='fu'>count_susceptible</span><span class='op'>(</span><span class='va'>GEN</span><span class='op'>)</span> <span class='co'># 1399</span>
|
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<span class='va'>example_isolates</span> <span class='op'>%>%</span> <span class='fu'>count_all</span><span class='op'>(</span><span class='va'>GEN</span><span class='op'>)</span> <span class='co'># 1855</span>
|
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<span class='kw'>example_isolates</span> <span class='op'>%>%</span> <span class='fu'>count_susceptible</span>(<span class='kw'>AMC</span>, <span class='kw'>GEN</span>) <span class='co'># 1764</span>
|
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<span class='kw'>example_isolates</span> <span class='op'>%>%</span> <span class='fu'>count_all</span>(<span class='kw'>AMC</span>, <span class='kw'>GEN</span>) <span class='co'># 1936</span>
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<span class='va'>example_isolates</span> <span class='op'>%>%</span> <span class='fu'>count_susceptible</span><span class='op'>(</span><span class='va'>AMC</span>, <span class='va'>GEN</span><span class='op'>)</span> <span class='co'># 1764</span>
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<span class='va'>example_isolates</span> <span class='op'>%>%</span> <span class='fu'>count_all</span><span class='op'>(</span><span class='va'>AMC</span>, <span class='va'>GEN</span><span class='op'>)</span> <span class='co'># 1936</span>
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<span class='co'># Get number of S+I vs. R immediately of selected columns</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'>AMX</span>, <span class='kw'>CIP</span>) <span class='op'>%>%</span>
|
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<span class='fu'>count_df</span>(translate = <span class='fl'>FALSE</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'>AMX</span>, <span class='va'>CIP</span><span class='op'>)</span> <span class='op'>%>%</span>
|
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<span class='fu'>count_df</span><span class='op'>(</span>translate <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
|
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|
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<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'>count_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'>count_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">
|
||||
@ -449,7 +449,7 @@ 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