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(v1.4.0.9013) is_gram_negative/positive update

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dr. M.S. (Matthijs) Berends
2020-11-09 13:07:02 +01:00
parent 423879c034
commit d3b1d33210
22 changed files with 149 additions and 82 deletions
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4
docs/reference/antibiotic_class_selectors.html
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@ -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>
@ -315,7 +315,7 @@
<span class='co'># get bug/drug combinations for only macrolides in Gram-positives:</span>
<span class='va'>example_isolates</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span><span class='op'>(</span><span class='va'>mo</span> <span class='op'>%&gt;%</span> <span class='fu'><a href='mo_property.html'>is_gram_positive</a></span><span class='op'>(</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span><span class='op'>(</span><span class='fu'><a href='mo_property.html'>is_gram_positive</a></span><span class='op'>(</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span><span class='op'>(</span><span class='va'>mo</span>, <span class='fu'>macrolides</span><span class='op'>(</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='bug_drug_combinations.html'>bug_drug_combinations</a></span><span class='op'>(</span><span class='op'>)</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://rdrr.io/r/base/format.html'>format</a></span><span class='op'>(</span><span class='op'>)</span>

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docs/reference/as.mo.html
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@ -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>
@ -270,7 +270,7 @@
</tr>
<tr>
<th>Becker</th>
<td><p>a logical to indicate whether <em>Staphylococci</em> should be categorised into coagulase-negative <em>Staphylococci</em> ("CoNS") and coagulase-positive <em>Staphylococci</em> ("CoPS") instead of their own species, according to Karsten Becker <em>et al.</em> (1,2,3).</p>
<td><p>a logical to indicate whether staphylococci should be categorised into coagulase-negative staphylococci ("CoNS") and coagulase-positive staphylococci ("CoPS") instead of their own species, according to Karsten Becker <em>et al.</em> (1,2,3).</p>
<p>This excludes <em>Staphylococcus aureus</em> at default, use <code>Becker = "all"</code> to also categorise <em>S. aureus</em> as "CoPS".</p></td>
</tr>
<tr>

2
docs/reference/index.html
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@ -81,7 +81,7 @@
</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">1.4.0.9012</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9013</span>
</span>
</div>

10
docs/reference/mo_property.html
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@ -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>