mo codes for WHONET

docs/reference/as.mo.html

@@ -237,7 +237,13 @@
     <pre class="usage"><span class='fu'>as.mo</span>(<span class='no'>x</span>, <span class='kw'>Becker</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>Lancefield</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>allow_uncertain</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
   <span class='kw'>reference_df</span> <span class='kw'>=</span> <span class='fu'><a href='mo_source.html'>get_mo_source</a></span>())
 
-<span class='fu'>is.mo</span>(<span class='no'>x</span>)</pre>
+<span class='fu'>is.mo</span>(<span class='no'>x</span>)
+
+<span class='fu'>mo_failures</span>()
+
+<span class='fu'>mo_uncertainties</span>()
+
+<span class='fu'>mo_renamed</span>()</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
     <table class="ref-arguments">
@@ -287,7 +293,7 @@
 </pre>
     <p>Use the <code><a href='mo_property.html'>mo_property</a></code> functions to get properties based on the returned code, see Examples.</p>
 <p>This function uses Artificial Intelligence (AI) to help getting fast and logical results. It tries to find matches in this order:</p><ul>
-<li><p>Taxonomic kingdom: it first searches in bacteria, then fungi, then protozoa</p></li>
+<li><p>Taxonomic kingdom: it first searches in Bacteria, then Fungi, then Protozoa</p></li>
 <li><p>Human pathogenic prevalence: it first searches in more prevalent microorganisms, then less prevalent ones</p></li>
 <li><p>Valid MO codes and full names: it first searches in already valid MO code and known genus/species combinations</p></li>
 <li><p>Breakdown of input values: from here it starts to breakdown input values to find possible matches</p></li>
@@ -298,11 +304,23 @@
 <li><p>Something like <code>"p aer"</code> will return the ID of <em>Pseudomonas aeruginosa</em> and not <em>Pasteurella aerogenes</em></p></li>
 <li><p>Something like <code>"stau"</code> or <code>"S aur"</code> will return the ID of <em>Staphylococcus aureus</em> and not <em>Staphylococcus auricularis</em></p></li>
 </ul><p>This means that looking up human pathogenic microorganisms takes less time than looking up human <strong>non</strong>-pathogenic microorganisms.</p>
-<p>When using <code>allow_uncertain = TRUE</code> (which is the default setting), it will use additional rules if all previous AI rules failed to get valid results. Examples:</p><ul>
+<p><strong>UNCERTAIN RESULTS</strong> <br />
+When using <code>allow_uncertain = TRUE</code> (which is the default setting), it will use additional rules if all previous AI rules failed to get valid results. These are:</p><ul>
+<li><p>It tries to look for previously accepted (but now invalid) taxonomic names</p></li>
+<li><p>It strips off values between brackets and the brackets itself, and re-evaluates the input with all previous rules</p></li>
+<li><p>It strips off words from the end one by one and re-evaluates the input with all previous rules</p></li>
+<li><p>It strips off words from the start one by one and re-evaluates the input with all previous rules</p></li>
+<li><p>It tries to look for some manual changes which are not yet published to the ITIS database (like <em>Propionibacterium</em> not yet being <em>Cutibacterium</em>)</p></li>
+</ul>
+    <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_STRPTC_GRB</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>"D. spartina"</code>. This is the abbreviation of an old taxonomic name: <em>Didymosphaeria spartinae</em> (the last "e" was missing from the input). This fungus was renamed to <em>Leptosphaeria obiones</em>, so a warning will be thrown that this result (<code>F_LPTSP_OBI</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>
+    <p>Use <code>mo_failures()</code> to get a vector with all values that could not be coerced to a valid value.</p>
+<p>Use <code>mo_uncertainties()</code> to get a vector with all values that were coerced to a valid value, but with uncertainty.</p>
+<p>Use <code>mo_renamed()</code> to get a vector with all values that could be coerced based on an old, previously accepted taxonomic name.</p>
     
     <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>