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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/bug_drug_combinations.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>
@ -242,22 +242,22 @@
<p>Determine antimicrobial resistance (AMR) of all bug-drug combinations in your data set where at least 30 (default) isolates are available per species. Use <code><a href='https://rdrr.io/r/base/format.html'>format()</a></code> on the result to prettify it to a publicable/printable format, see Examples.</p>
</div>
<pre class="usage"><span class='fu'>bug_drug_combinations</span>(<span class='kw'>x</span>, col_mo = <span class='kw'>NULL</span>, FUN = <span class='kw'>mo_shortname</span>, <span class='kw'>...</span>)
<pre class="usage"><span class='fu'>bug_drug_combinations</span><span class='op'>(</span><span class='va'>x</span>, col_mo <span class='op'>=</span> <span class='cn'>NULL</span>, FUN <span class='op'>=</span> <span class='va'>mo_shortname</span>, <span class='va'>...</span><span class='op'>)</span>
<span class='co'># S3 method for bug_drug_combinations</span>
<span class='fu'><a href='https://rdrr.io/r/base/format.html'>format</a></span>(
<span class='kw'>x</span>,
translate_ab = <span class='st'>"name (ab, atc)"</span>,
language = <span class='fu'><a href='translate.html'>get_locale</a></span>(),
minimum = <span class='fl'>30</span>,
combine_SI = <span class='fl'>TRUE</span>,
combine_IR = <span class='fl'>FALSE</span>,
add_ab_group = <span class='fl'>TRUE</span>,
remove_intrinsic_resistant = <span class='fl'>FALSE</span>,
decimal.mark = <span class='fu'><a href='https://rdrr.io/r/base/options.html'>getOption</a></span>(<span class='st'>"OutDec"</span>),
big.mark = <span class='fu'><a href='https://rdrr.io/r/base/ifelse.html'>ifelse</a></span>(<span class='kw'>decimal.mark</span> <span class='op'>==</span> <span class='st'>","</span>, <span class='st'>"."</span>, <span class='st'>","</span>),
<span class='kw'>...</span>
)</pre>
<span class='fu'><a href='https://rdrr.io/r/base/format.html'>format</a></span><span class='op'>(</span>
<span class='va'>x</span>,
translate_ab <span class='op'>=</span> <span class='st'>"name (ab, atc)"</span>,
language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>,
minimum <span class='op'>=</span> <span class='fl'>30</span>,
combine_SI <span class='op'>=</span> <span class='cn'>TRUE</span>,
combine_IR <span class='op'>=</span> <span class='cn'>FALSE</span>,
add_ab_group <span class='op'>=</span> <span class='cn'>TRUE</span>,
remove_intrinsic_resistant <span class='op'>=</span> <span class='cn'>FALSE</span>,
decimal.mark <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/options.html'>getOption</a></span><span class='op'>(</span><span class='st'>"OutDec"</span><span class='op'>)</span>,
big.mark <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/ifelse.html'>ifelse</a></span><span class='op'>(</span><span class='va'>decimal.mark</span> <span class='op'>==</span> <span class='st'>","</span>, <span class='st'>"."</span>, <span class='st'>","</span><span class='op'>)</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">
@ -343,18 +343,18 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='co'># \donttest{</span>
<span class='kw'>x</span> <span class='op'>&lt;-</span> <span class='fu'>bug_drug_combinations</span>(<span class='kw'>example_isolates</span>)
<span class='kw'>x</span>
<span class='fu'><a href='https://rdrr.io/r/base/format.html'>format</a></span>(<span class='kw'>x</span>, translate_ab = <span class='st'>"name (atc)"</span>)
<span class='va'>x</span> <span class='op'>&lt;-</span> <span class='fu'>bug_drug_combinations</span><span class='op'>(</span><span class='va'>example_isolates</span><span class='op'>)</span>
<span class='va'>x</span>
<span class='fu'><a href='https://rdrr.io/r/base/format.html'>format</a></span><span class='op'>(</span><span class='va'>x</span>, translate_ab <span class='op'>=</span> <span class='st'>"name (atc)"</span><span class='op'>)</span>
<span class='co'># Use FUN to change to transformation of microorganism codes</span>
<span class='fu'>bug_drug_combinations</span>(<span class='kw'>example_isolates</span>,
FUN = <span class='kw'>mo_gramstain</span>)
<span class='fu'>bug_drug_combinations</span><span class='op'>(</span><span class='va'>example_isolates</span>,
FUN <span class='op'>=</span> <span class='va'>mo_gramstain</span><span class='op'>)</span>
<span class='fu'>bug_drug_combinations</span>(<span class='kw'>example_isolates</span>,
FUN = <span class='fu'>function</span>(<span class='kw'>x</span>) <span class='fu'><a href='https://rdrr.io/r/base/ifelse.html'>ifelse</a></span>(<span class='kw'>x</span> <span class='op'>==</span> <span class='fu'><a href='as.mo.html'>as.mo</a></span>(<span class='st'>"E. coli"</span>),
<span class='fu'>bug_drug_combinations</span><span class='op'>(</span><span class='va'>example_isolates</span>,
FUN <span class='op'>=</span> <span class='kw'>function</span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span> <span class='fu'><a href='https://rdrr.io/r/base/ifelse.html'>ifelse</a></span><span class='op'>(</span><span class='va'>x</span> <span class='op'>==</span> <span class='fu'><a href='as.mo.html'>as.mo</a></span><span class='op'>(</span><span class='st'>"E. coli"</span><span class='op'>)</span>,
<span class='st'>"E. coli"</span>,
<span class='st'>"Others"</span>))
<span class='st'>"Others"</span><span class='op'>)</span><span class='op'>)</span>
<span class='co'># }</span>
</pre>
</div>
@ -372,7 +372,7 @@ 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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