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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/mo_source.html
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@ -83,7 +83,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
</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>
@ -244,9 +244,9 @@ This is the fastest way to have your organisation (or analysis) specific codes p
<p>This is <strong>the fastest way</strong> to have your organisation (or analysis) specific codes picked up and translated by this package.</p>
</div>
<pre class="usage"><span class='fu'>set_mo_source</span>(<span class='kw'>path</span>)
<pre class="usage"><span class='fu'>set_mo_source</span><span class='op'>(</span><span class='va'>path</span><span class='op'>)</span>
<span class='fu'>get_mo_source</span>()</pre>
<span class='fu'>get_mo_source</span><span class='op'>(</span><span class='op'>)</span></pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@ -277,20 +277,20 @@ This is the fastest way to have your organisation (or analysis) specific codes p
4 | | |
</pre>
<p>We save it as <code>"home/me/ourcodes.xlsx"</code>. Now we have to set it as a source:</p><pre><span class='fu'>set_mo_source</span>(<span class='st'>"home/me/ourcodes.xlsx"</span>)
<p>We save it as <code>"home/me/ourcodes.xlsx"</code>. Now we have to set it as a source:</p><pre><span class='fu'>set_mo_source</span><span class='op'>(</span><span class='st'>"home/me/ourcodes.xlsx"</span><span class='op'>)</span>
<span class='co'>#&gt; NOTE: Created mo_source file '~/.mo_source.rds' from 'home/me/ourcodes.xlsx'</span>
<span class='co'>#&gt; (columns "Organisation XYZ" and "mo")</span>
</pre>
<p>It has now created a file <code>"~/.mo_source.rds"</code> with the contents of our Excel file. Only the first column with foreign values and the 'mo' column will be kept when creating the RDS file.</p>
<p>And now we can use it in our functions:</p><pre><span class='fu'><a href='as.mo.html'>as.mo</a></span>(<span class='st'>"lab_mo_ecoli"</span>)
<p>And now we can use it in our functions:</p><pre><span class='fu'><a href='as.mo.html'>as.mo</a></span><span class='op'>(</span><span class='st'>"lab_mo_ecoli"</span><span class='op'>)</span>
<span class='co'>#&gt; [1] B_ESCHR_COLI</span>
<span class='fu'><a href='mo_property.html'>mo_genus</a></span>(<span class='st'>"lab_mo_kpneumoniae"</span>)
<span class='fu'><a href='mo_property.html'>mo_genus</a></span><span class='op'>(</span><span class='st'>"lab_mo_kpneumoniae"</span><span class='op'>)</span>
<span class='co'>#&gt; [1] "Klebsiella"</span>
<span class='co'># other input values still work too</span>
<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'>"Escherichia coli"</span>, <span class='st'>"E. coli"</span>, <span class='st'>"lab_mo_ecoli"</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'>"Escherichia coli"</span>, <span class='st'>"E. coli"</span>, <span class='st'>"lab_mo_ecoli"</span><span class='op'>)</span><span class='op'>)</span>
<span class='co'>#&gt; [1] B_ESCHR_COLI B_ESCHR_COLI B_ESCHR_COLI</span>
</pre>
@ -303,16 +303,16 @@ This is the fastest way to have your organisation (or analysis) specific codes p
5 | | |
</pre>
<p>...any new usage of an MO function in this package will update your data file:</p><pre><span class='fu'><a href='as.mo.html'>as.mo</a></span>(<span class='st'>"lab_mo_ecoli"</span>)
<p>...any new usage of an MO function in this package will update your data file:</p><pre><span class='fu'><a href='as.mo.html'>as.mo</a></span><span class='op'>(</span><span class='st'>"lab_mo_ecoli"</span><span class='op'>)</span>
<span class='co'>#&gt; NOTE: Updated mo_source file '~/.mo_source.rds' from 'home/me/ourcodes.xlsx'</span>
<span class='co'>#&gt; (columns "Organisation XYZ" and "mo")</span>
<span class='co'>#&gt; [1] B_ESCHR_COLI</span>
<span class='fu'><a href='mo_property.html'>mo_genus</a></span>(<span class='st'>"lab_Staph_aureus"</span>)
<span class='fu'><a href='mo_property.html'>mo_genus</a></span><span class='op'>(</span><span class='st'>"lab_Staph_aureus"</span><span class='op'>)</span>
<span class='co'>#&gt; [1] "Staphylococcus"</span>
</pre>
<p>To delete the reference data file, just use <code>""</code>, <code>NULL</code> or <code>FALSE</code> as input for <code>set_mo_source()</code>:</p><pre><span class='fu'>set_mo_source</span>(<span class='kw'>NULL</span>)
<p>To delete the reference data file, just use <code>""</code>, <code>NULL</code> or <code>FALSE</code> as input for <code>set_mo_source()</code>:</p><pre><span class='fu'>set_mo_source</span><span class='op'>(</span><span class='cn'>NULL</span><span class='op'>)</span>
<span class='co'># Removed mo_source file '~/.mo_source.rds'.</span>
</pre>
@ -345,7 +345,7 @@ 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>
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