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(v0.7.1.9075) new microorganism codes

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dr. M.S. (Matthijs) Berends
2019-09-18 15:46:09 +02:00
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docs/reference/as.mo.html
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@ -80,7 +80,7 @@
</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">0.7.1.9073</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9075</span>
</span>
</div>
@ -266,7 +266,7 @@
</tr>
<tr>
<th>allow_uncertain</th>
<td><p>a number between 0 (or "none") and 3 (or "all"), or TRUE (= 2) or FALSE (= 0) to indicate whether the input should be checked for less possible results, see Details</p></td>
<td><p>a number between 0 (or "none") and 3 (or "all"), or TRUE (= 2) or FALSE (= 0) to indicate whether the input should be checked for less probable results, see Details</p></td>
</tr>
<tr>
<th>reference_df</th>
@ -286,16 +286,16 @@
<p><strong>General info</strong> <br />
A microorganism ID from this package (class: <code>mo</code>) typically looks like these examples:<br /></p><pre>
Code Full name
--------------- --------------------------------------
B_KLBSL Klebsiella
B_KLBSL_PNE Klebsiella pneumoniae
B_KLBSL_PNE_RHI Klebsiella pneumoniae rhinoscleromatis
| | | |
| | | |
| | | ----&gt; subspecies, a 3-4 letter acronym
| | ----&gt; species, a 3-4 letter acronym
| ----&gt; genus, a 5-7 letter acronym, mostly without vowels
Code Full name
--------------- --------------------------------------
B_KLBSL Klebsiella
B_KLBSL_PNMN Klebsiella pneumoniae
B_KLBSL_PNMN_RHNS Klebsiella pneumoniae rhinoscleromatis
| | | |
| | | |
| | | ---&gt; subspecies, a 4-5 letter acronym
| | ----&gt; species, a 4-5 letter acronym
| ----&gt; genus, a 5-7 letter acronym
----&gt; taxonomic kingdom: A (Archaea), AN (Animalia), B (Bacteria),
C (Chromista), F (Fungi), P (Protozoa)
</pre>
@ -325,7 +325,7 @@ The algorithm can additionally use three different levels of uncertainty to gues
</ul>
<p>You can also use e.g. <code>as.mo(..., allow_uncertain = 1)</code> to only allow up to level 1 uncertainty.</p>
<p>Examples:</p><ul>
<li><p><code>"Streptococcus group B (known as S. agalactiae)"</code>. The text between brackets will be removed and a warning will be thrown that the result <em>Streptococcus group B</em> (<code>B_STRPT_GRB</code>) needs review.</p></li>
<li><p><code>"Streptococcus group B (known as S. agalactiae)"</code>. The text between brackets will be removed and a warning will be thrown that the result <em>Streptococcus group B</em> (<code>B_STRPT_GRPB</code>) needs review.</p></li>
<li><p><code>"S. aureus - please mind: MRSA"</code>. The last word will be stripped, after which the function will try to find a match. If it does not, the second last word will be stripped, etc. Again, a warning will be thrown that the result <em>Staphylococcus aureus</em> (<code>B_STPHY_AUR</code>) needs review.</p></li>
<li><p><code>"Fluoroquinolone-resistant Neisseria gonorrhoeae"</code>. The first word will be stripped, after which the function will try to find a match. A warning will be thrown that the result <em>Neisseria gonorrhoeae</em> (<code>B_NESSR_GON</code>) needs review.</p></li>
</ul>
@ -369,7 +369,7 @@ 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='co'># These examples all return "B_STPHY_AURS", the ID of S. aureus:</span>
<span class='fu'>as.mo</span>(<span class='st'>"sau"</span>) <span class='co'># WHONET code</span>
<span class='fu'>as.mo</span>(<span class='st'>"stau"</span>)
<span class='fu'>as.mo</span>(<span class='st'>"STAU"</span>)
@ -394,11 +394,11 @@ The <code><a href='mo_property.html'>mo_property</a></code> functions (like <cod
<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>
<span class='fu'>as.mo</span>(<span class='st'>"S. epidermidis"</span>) <span class='co'># will remain species: B_STPHY_EPI</span>
<span class='fu'>as.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'>as.mo</span>(<span class='st'>"S. epidermidis"</span>) <span class='co'># will remain species: B_STPHY_EPDR</span>
<span class='fu'>as.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_CONS</span>
<span class='fu'>as.mo</span>(<span class='st'>"S. pyogenes"</span>) <span class='co'># will remain species: B_STRPT_PYO</span>
<span class='fu'>as.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_STRPT_GRA</span>
<span class='fu'>as.mo</span>(<span class='st'>"S. pyogenes"</span>) <span class='co'># will remain species: B_STRPT_PYGN</span>
<span class='fu'>as.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_STRPT_GRPA</span>
<span class='co'># All mo_* functions use as.mo() internally too (see ?mo_property):</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>