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(v1.4.0.9000) more extensive unit tests

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dr. M.S. (Matthijs) Berends
2020-10-15 09:46:41 +02:00
parent 28e77680c5
commit 833a1be36d
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docs/reference/join.html
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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">1.4.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9000</span>
</span>
</div>
@ -242,17 +242,17 @@
<p>Join the data set <a href='microorganisms.html'>microorganisms</a> easily to an existing table or character vector.</p>
</div>
<pre class="usage"><span class='fu'>inner_join_microorganisms</span>(<span class='kw'>x</span>, by = <span class='kw'>NULL</span>, suffix = <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"2"</span>, <span class='st'>""</span>), <span class='kw'>...</span>)
<pre class="usage"><span class='fu'>inner_join_microorganisms</span><span class='op'>(</span><span class='va'>x</span>, by <span class='op'>=</span> <span class='cn'>NULL</span>, suffix <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'>"2"</span>, <span class='st'>""</span><span class='op'>)</span>, <span class='va'>...</span><span class='op'>)</span>
<span class='fu'>left_join_microorganisms</span>(<span class='kw'>x</span>, by = <span class='kw'>NULL</span>, suffix = <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"2"</span>, <span class='st'>""</span>), <span class='kw'>...</span>)
<span class='fu'>left_join_microorganisms</span><span class='op'>(</span><span class='va'>x</span>, by <span class='op'>=</span> <span class='cn'>NULL</span>, suffix <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'>"2"</span>, <span class='st'>""</span><span class='op'>)</span>, <span class='va'>...</span><span class='op'>)</span>
<span class='fu'>right_join_microorganisms</span>(<span class='kw'>x</span>, by = <span class='kw'>NULL</span>, suffix = <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"2"</span>, <span class='st'>""</span>), <span class='kw'>...</span>)
<span class='fu'>right_join_microorganisms</span><span class='op'>(</span><span class='va'>x</span>, by <span class='op'>=</span> <span class='cn'>NULL</span>, suffix <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'>"2"</span>, <span class='st'>""</span><span class='op'>)</span>, <span class='va'>...</span><span class='op'>)</span>
<span class='fu'>full_join_microorganisms</span>(<span class='kw'>x</span>, by = <span class='kw'>NULL</span>, suffix = <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"2"</span>, <span class='st'>""</span>), <span class='kw'>...</span>)
<span class='fu'>full_join_microorganisms</span><span class='op'>(</span><span class='va'>x</span>, by <span class='op'>=</span> <span class='cn'>NULL</span>, suffix <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'>"2"</span>, <span class='st'>""</span><span class='op'>)</span>, <span class='va'>...</span><span class='op'>)</span>
<span class='fu'>semi_join_microorganisms</span>(<span class='kw'>x</span>, by = <span class='kw'>NULL</span>, <span class='kw'>...</span>)
<span class='fu'>semi_join_microorganisms</span><span class='op'>(</span><span class='va'>x</span>, by <span class='op'>=</span> <span class='cn'>NULL</span>, <span class='va'>...</span><span class='op'>)</span>
<span class='fu'>anti_join_microorganisms</span>(<span class='kw'>x</span>, by = <span class='kw'>NULL</span>, <span class='kw'>...</span>)</pre>
<span class='fu'>anti_join_microorganisms</span><span class='op'>(</span><span class='va'>x</span>, by <span class='op'>=</span> <span class='cn'>NULL</span>, <span class='va'>...</span><span class='op'>)</span></pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@ -293,25 +293,25 @@ 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 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="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='fu'>left_join_microorganisms</span>(<span class='fu'><a href='as.mo.html'>as.mo</a></span>(<span class='st'>"K. pneumoniae"</span>))
<span class='fu'>left_join_microorganisms</span>(<span class='st'>"B_KLBSL_PNE"</span>)
<pre class="examples"><span class='fu'>left_join_microorganisms</span><span class='op'>(</span><span class='fu'><a href='as.mo.html'>as.mo</a></span><span class='op'>(</span><span class='st'>"K. pneumoniae"</span><span class='op'>)</span><span class='op'>)</span>
<span class='fu'>left_join_microorganisms</span><span class='op'>(</span><span class='st'>"B_KLBSL_PNE"</span><span class='op'>)</span>
<span class='co'># \donttest{</span>
<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>)) {
<span class='kw'>example_isolates</span> <span class='op'>%&gt;%</span>
<span class='fu'>left_join_microorganisms</span>() <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://rdrr.io/r/base/colnames.html'>colnames</a></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='va'>example_isolates</span> <span class='op'>%&gt;%</span>
<span class='fu'>left_join_microorganisms</span><span class='op'>(</span><span class='op'>)</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://rdrr.io/r/base/colnames.html'>colnames</a></span><span class='op'>(</span><span class='op'>)</span>
<span class='kw'>df</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span>(date = <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span>(from = <span class='fu'><a href='https://rdrr.io/r/base/as.Date.html'>as.Date</a></span>(<span class='st'>"2018-01-01"</span>),
to = <span class='fu'><a href='https://rdrr.io/r/base/as.Date.html'>as.Date</a></span>(<span class='st'>"2018-01-07"</span>),
by = <span class='fl'>1</span>),
bacteria = <span class='fu'><a href='as.mo.html'>as.mo</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"S. aureus"</span>, <span class='st'>"MRSA"</span>, <span class='st'>"MSSA"</span>, <span class='st'>"STAAUR"</span>,
<span class='st'>"E. coli"</span>, <span class='st'>"E. coli"</span>, <span class='st'>"E. coli"</span>)),
stringsAsFactors = <span class='fl'>FALSE</span>)
<span class='fu'><a href='https://rdrr.io/r/base/colnames.html'>colnames</a></span>(<span class='kw'>df</span>)
<span class='kw'>df_joined</span> <span class='op'>&lt;-</span> <span class='fu'>left_join_microorganisms</span>(<span class='kw'>df</span>, <span class='st'>"bacteria"</span>)
<span class='fu'><a href='https://rdrr.io/r/base/colnames.html'>colnames</a></span>(<span class='kw'>df_joined</span>)
}
<span class='va'>df</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span><span class='op'>(</span>date <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span><span class='op'>(</span>from <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/as.Date.html'>as.Date</a></span><span class='op'>(</span><span class='st'>"2018-01-01"</span><span class='op'>)</span>,
to <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/as.Date.html'>as.Date</a></span><span class='op'>(</span><span class='st'>"2018-01-07"</span><span class='op'>)</span>,
by <span class='op'>=</span> <span class='fl'>1</span><span class='op'>)</span>,
bacteria <span class='op'>=</span> <span class='fu'><a href='as.mo.html'>as.mo</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='st'>"S. aureus"</span>, <span class='st'>"MRSA"</span>, <span class='st'>"MSSA"</span>, <span class='st'>"STAAUR"</span>,
<span class='st'>"E. coli"</span>, <span class='st'>"E. coli"</span>, <span class='st'>"E. coli"</span><span class='op'>)</span><span class='op'>)</span>,
stringsAsFactors <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
<span class='fu'><a href='https://rdrr.io/r/base/colnames.html'>colnames</a></span><span class='op'>(</span><span class='va'>df</span><span class='op'>)</span>
<span class='va'>df_joined</span> <span class='op'>&lt;-</span> <span class='fu'>left_join_microorganisms</span><span class='op'>(</span><span class='va'>df</span>, <span class='st'>"bacteria"</span><span class='op'>)</span>
<span class='fu'><a href='https://rdrr.io/r/base/colnames.html'>colnames</a></span><span class='op'>(</span><span class='va'>df_joined</span><span class='op'>)</span>
<span class='op'>}</span>
<span class='co'># }</span>
</pre>
</div>
@ -329,7 +329,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
</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>
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