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@ -263,41 +263,37 @@ The <code><a href='mo_property.html'>mo_property</a></code> functions (like <cod
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='co'># NOT RUN {</span>
<span class='co'># These examples all return "B_STPHY_AUR", the ID of S. aureus:</span>
<span class='fu'>as.mo</span>(<span class='st'>"stau"</span>)
<span class='fu'>as.mo</span>(<span class='st'>"STAU"</span>)
<span class='fu'>as.mo</span>(<span class='st'>"staaur"</span>)
<span class='fu'>as.mo</span>(<span class='st'>"S. aureus"</span>)
<span class='fu'>as.mo</span>(<span class='st'>"S aureus"</span>)
<span class='fu'>as.mo</span>(<span class='st'>"Staphylococcus aureus"</span>)
<span class='fu'>as.mo</span>(<span class='st'>"Staphylococcus aureus (MRSA)"</span>)
<span class='fu'>as.mo</span>(<span class='st'>"MRSA"</span>) <span class='co'># Methicillin Resistant S. aureus</span>
<span class='fu'>as.mo</span>(<span class='st'>"VISA"</span>) <span class='co'># Vancomycin Intermediate S. aureus</span>
<span class='fu'>as.mo</span>(<span class='st'>"VRSA"</span>) <span class='co'># Vancomycin Resistant S. aureus</span>
<span class='fu'>as.mo</span>(<span class='fl'>369</span>) <span class='co'># Search on TSN (Taxonomic Serial Number), a unique identifier</span>
<span class='co'># for the Integrated Taxonomic Information System (ITIS)</span>
<span class='fu'>as.mo</span>(<span class='st'>"Streptococcus group A"</span>)
<span class='fu'>as.mo</span>(<span class='st'>"GAS"</span>) <span class='co'># Group A Streptococci</span>
<span class='fu'>as.mo</span>(<span class='st'>"GBS"</span>) <span class='co'># Group B Streptococci</span>
<pre class="examples"><div class='input'><span class='co'># These examples all return "B_STPHY_AUR", the ID of S. aureus:</span>
<span class='fu'>as.mo</span>(<span class='st'>"stau"</span>)</div><div class='output co'>#&gt; Class 'mo'
#&gt; [1] B_STPHY_AUR</div><div class='input'><span class='fu'>as.mo</span>(<span class='st'>"STAU"</span>)</div><div class='output co'>#&gt; Class 'mo'
#&gt; [1] B_STPHY_AUR</div><div class='input'><span class='fu'>as.mo</span>(<span class='st'>"staaur"</span>)</div><div class='output co'>#&gt; Class 'mo'
#&gt; [1] B_STPHY_AUR</div><div class='input'><span class='fu'>as.mo</span>(<span class='st'>"S. aureus"</span>)</div><div class='output co'>#&gt; Class 'mo'
#&gt; [1] B_STPHY_AUR</div><div class='input'><span class='fu'>as.mo</span>(<span class='st'>"S aureus"</span>)</div><div class='output co'>#&gt; Class 'mo'
#&gt; [1] B_STPHY_AUR</div><div class='input'><span class='fu'>as.mo</span>(<span class='st'>"Staphylococcus aureus"</span>)</div><div class='output co'>#&gt; Class 'mo'
#&gt; [1] B_STPHY_AUR</div><div class='input'><span class='fu'>as.mo</span>(<span class='st'>"Staphylococcus aureus (MRSA)"</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: <span style='color: #BB0000;'>UNCERTAIN - "Staphylococcus aureus (MRSA)" -&gt; </span><span style='color: #BB0000;font-style: italic;'>Staphylococcus aureus</span><span style='color: #BB0000;'> (B_STPHY_AUR)</span><span></span></div><div class='output co'>#&gt; Class 'mo'
#&gt; [1] B_STPHY_AUR</div><div class='input'><span class='fu'>as.mo</span>(<span class='st'>"MRSA"</span>) <span class='co'># Methicillin Resistant S. aureus</span></div><div class='output co'>#&gt; Class 'mo'
#&gt; [1] B_STPHY_AUR</div><div class='input'><span class='fu'>as.mo</span>(<span class='st'>"VISA"</span>) <span class='co'># Vancomycin Intermediate S. aureus</span></div><div class='output co'>#&gt; Class 'mo'
#&gt; [1] B_STPHY_AUR</div><div class='input'><span class='fu'>as.mo</span>(<span class='st'>"VRSA"</span>) <span class='co'># Vancomycin Resistant S. aureus</span></div><div class='output co'>#&gt; Class 'mo'
#&gt; [1] B_STPHY_AUR</div><div class='input'><span class='fu'>as.mo</span>(<span class='fl'>369</span>) <span class='co'># Search on TSN (Taxonomic Serial Number), a unique identifier</span></div><div class='output co'>#&gt; Class 'mo'
#&gt; [1] B_STPHY_AUR</div><div class='input'> <span class='co'># for the Integrated Taxonomic Information System (ITIS)</span>
<span class='fu'>as.mo</span>(<span class='st'>"Streptococcus group A"</span>)</div><div class='output co'>#&gt; Class 'mo'
#&gt; [1] B_STRPTC_GRA</div><div class='input'><span class='fu'>as.mo</span>(<span class='st'>"GAS"</span>) <span class='co'># Group A Streptococci</span></div><div class='output co'>#&gt; Class 'mo'
#&gt; [1] B_STRPTC_GRA</div><div class='input'><span class='fu'>as.mo</span>(<span class='st'>"GBS"</span>) <span class='co'># Group B Streptococci</span></div><div class='output co'>#&gt; Class 'mo'
#&gt; [1] B_STRPTC_GRB</div><div class='input'>
<span class='co'># guess_mo is an alias of as.mo and works the same</span>
<span class='fu'>guess_mo</span>(<span class='st'>"S. epidermidis"</span>) <span class='co'># will remain species: B_STPHY_EPI</span>
<span class='fu'>guess_mo</span>(<span class='st'>"S. epidermidis"</span>, <span class='kw'>Becker</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='co'># will not remain species: B_STPHY_CNS</span>
<span class='fu'>guess_mo</span>(<span class='st'>"S. pyogenes"</span>) <span class='co'># will remain species: B_STRPTC_PYO</span>
<span class='fu'>guess_mo</span>(<span class='st'>"S. pyogenes"</span>, <span class='kw'>Lancefield</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='co'># will not remain species: B_STRPTC_GRA</span>
<span class='fu'>guess_mo</span>(<span class='st'>"S. epidermidis"</span>) <span class='co'># will remain species: B_STPHY_EPI</span></div><div class='output co'>#&gt; Class 'mo'
#&gt; [1] B_STPHY_EPI</div><div class='input'><span class='fu'>guess_mo</span>(<span class='st'>"S. epidermidis"</span>, <span class='kw'>Becker</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='co'># will not remain species: B_STPHY_CNS</span></div><div class='output co'>#&gt; Class 'mo'
#&gt; [1] B_STPHY_CNS</div><div class='input'>
<span class='fu'>guess_mo</span>(<span class='st'>"S. pyogenes"</span>) <span class='co'># will remain species: B_STRPTC_PYO</span></div><div class='output co'>#&gt; Class 'mo'
#&gt; [1] B_STRPTC_PYO</div><div class='input'><span class='fu'>guess_mo</span>(<span class='st'>"S. pyogenes"</span>, <span class='kw'>Lancefield</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='co'># will not remain species: B_STRPTC_GRA</span></div><div class='output co'>#&gt; Class 'mo'
#&gt; [1] B_STRPTC_GRA</div><div class='input'>
<span class='co'># Use mo_* functions to get a specific property based on `mo`</span>
<span class='no'>Ecoli</span> <span class='kw'>&lt;-</span> <span class='fu'>as.mo</span>(<span class='st'>"E. coli"</span>) <span class='co'># returns `B_ESCHR_COL`</span>
<span class='fu'><a href='mo_property.html'>mo_genus</a></span>(<span class='no'>Ecoli</span>) <span class='co'># returns "Escherichia"</span>
<span class='fu'><a href='mo_property.html'>mo_gramstain</a></span>(<span class='no'>Ecoli</span>) <span class='co'># returns "Gram negative"</span>
<span class='co'># but it uses as.mo internally too, so you could also just use:</span>
<span class='fu'><a href='mo_property.html'>mo_genus</a></span>(<span class='st'>"E. coli"</span>) <span class='co'># returns "Escherichia"</span>
<span class='fu'><a href='mo_property.html'>mo_genus</a></span>(<span class='no'>Ecoli</span>) <span class='co'># returns "Escherichia"</span></div><div class='output co'>#&gt; [1] "Escherichia"</div><div class='input'><span class='fu'><a href='mo_property.html'>mo_gramstain</a></span>(<span class='no'>Ecoli</span>) <span class='co'># returns "Gram negative"</span></div><div class='output co'>#&gt; [1] "Gram-negatief"</div><div class='input'><span class='co'># but it uses as.mo internally too, so you could also just use:</span>
<span class='fu'><a href='mo_property.html'>mo_genus</a></span>(<span class='st'>"E. coli"</span>) <span class='co'># returns "Escherichia"</span></div><div class='output co'>#&gt; [1] "Escherichia"</div><div class='input'>
<span class='co'># }</span><span class='co'># NOT RUN {</span>
</div></span><span class='co'># NOT RUN {</span>
<span class='no'>df</span>$<span class='no'>mo</span> <span class='kw'>&lt;-</span> <span class='fu'>as.mo</span>(<span class='no'>df</span>$<span class='no'>microorganism_name</span>)
<span class='co'># the select function of tidyverse is also supported:</span>