(v1.4.0.9013) is_gram_negative/positive update

docs/reference/mo_property.html

@@ -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">1.4.0.9008</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9013</span>
       </span>
     </div>
 
@@ -340,7 +340,7 @@
 
 <p>The short name - <code>mo_shortname()</code> - almost always returns the first character of the genus and the full species, like <code>"E. coli"</code>. Exceptions are abbreviations of staphylococci (like <em>"CoNS"</em>, Coagulase-Negative Staphylococci) and beta-haemolytic streptococci (like <em>"GBS"</em>, Group B Streptococci). Please bear in mind that e.g. <em>E. coli</em> could mean <em>Escherichia coli</em> (kingdom of Bacteria) as well as <em>Entamoeba coli</em> (kingdom of Protozoa). Returning to the full name will be done using <code><a href='as.mo.html'>as.mo()</a></code> internally, giving priority to bacteria and human pathogens, i.e. <code>"E. coli"</code> will be considered <em>Escherichia coli</em>. In other words, <code>mo_fullname(mo_shortname("Entamoeba coli"))</code> returns <code>"Escherichia coli"</code>.</p>
 <p>Since the top-level of the taxonomy is sometimes referred to as 'kingdom' and sometimes as 'domain', the functions <code>mo_kingdom()</code> and <code>mo_domain()</code> return the exact same results.</p>
-<p>The Gram stain - <code>mo_gramstain()</code> - will be determined based on the taxonomic kingdom and phylum. According to Cavalier-Smith (2002, <a href='https://pubmed.ncbi.nlm.nih.gov/11837318'>PMID 11837318</a>), who defined subkingdoms Negibacteria and Posibacteria, only these phyla are Posibacteria: Actinobacteria, Chloroflexi, Firmicutes and Tenericutes. These bacteria are considered Gram-positive - all other bacteria are considered Gram-negative. Species outside the kingdom of Bacteria will return a value <code>NA</code>. Functions <code>is_gram_negative()</code> and <code>is_gram_positive()</code> always return <code>TRUE</code> or <code>FALSE</code>, even for species outside the kingdom of Bacteria.</p>
+<p>The Gram stain - <code>mo_gramstain()</code> - will be determined based on the taxonomic kingdom and phylum. According to Cavalier-Smith (2002, <a href='https://pubmed.ncbi.nlm.nih.gov/11837318'>PMID 11837318</a>), who defined subkingdoms Negibacteria and Posibacteria, only these phyla are Posibacteria: Actinobacteria, Chloroflexi, Firmicutes and Tenericutes. These bacteria are considered Gram-positive - all other bacteria are considered Gram-negative. Species outside the kingdom of Bacteria will return a value <code>NA</code>. Functions <code>is_gram_negative()</code> and <code>is_gram_positive()</code> always return <code>TRUE</code> or <code>FALSE</code> (except when the input is <code>NA</code> or the MO code is <code>UNKNOWN</code>), thus always return <code>FALSE</code> for species outside the taxonomic kingdom of Bacteria.</p>
 <p>All output will be <a href='translate.html'>translate</a>d where possible.</p>
 <p>The function <code>mo_url()</code> will return the direct URL to the online database entry, which also shows the scientific reference of the concerned species.</p>
     <h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable lifecycle</h2>
@@ -461,7 +461,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
 <span class='fu'>mo_shortname</span><span class='op'>(</span><span class='st'>"S. pyo"</span>, Lancefield <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> <span class='co'># "GAS" (='Group A Streptococci')</span>
 
 
-<span class='co'># language support for German, Dutch, Spanish, Portuguese, Italian and French</span>
+<span class='co'># language support  --------------------------------------------------------</span>
 <span class='fu'>mo_gramstain</span><span class='op'>(</span><span class='st'>"E. coli"</span>, language <span class='op'>=</span> <span class='st'>"de"</span><span class='op'>)</span>  <span class='co'># "Gramnegativ"</span>
 <span class='fu'>mo_gramstain</span><span class='op'>(</span><span class='st'>"E. coli"</span>, language <span class='op'>=</span> <span class='st'>"nl"</span><span class='op'>)</span>  <span class='co'># "Gram-negatief"</span>
 <span class='fu'>mo_gramstain</span><span class='op'>(</span><span class='st'>"E. coli"</span>, language <span class='op'>=</span> <span class='st'>"es"</span><span class='op'>)</span>  <span class='co'># "Gram negativo"</span>
@@ -478,7 +478,11 @@ This package contains the complete taxonomic tree of almost all microorganisms (
             Lancefield <span class='op'>=</span> <span class='cn'>TRUE</span>,
             language <span class='op'>=</span> <span class='st'>"nl"</span><span class='op'>)</span>              <span class='co'># "Streptococcus groep A"</span>
 
+<span class='co'># gram stains can be used as a filter</span>
+<span class='va'>example_isolates</span> <span class='op'>%&gt;%</span>
+  <span class='fu'><a href='https://rdrr.io/r/stats/filter.html'>filter</a></span><span class='op'>(</span><span class='fu'>is_gram_positive</span><span class='op'>(</span><span class='op'>)</span><span class='op'>)</span>
 
+<span class='co'># other --------------------------------------------------------------------</span>
 <span class='co'># get a list with the complete taxonomy (from kingdom to subspecies)</span>
 <span class='fu'>mo_taxonomy</span><span class='op'>(</span><span class='st'>"E. coli"</span><span class='op'>)</span>
 <span class='co'># get a list with the taxonomy, the authors, Gram-stain and URL to the online database</span>