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(v1.4.0.9000) more extensive unit tests
This commit is contained in:
@ -82,7 +82,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9000</span>
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</span>
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</div>
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@ -242,53 +242,53 @@
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<p>Use these functions to return a specific property of a microorganism based on the latest accepted taxonomy. All input values will be evaluated internally with <code><a href='as.mo.html'>as.mo()</a></code>, which makes it possible to use microbial abbreviations, codes and names as input. Please see <em>Examples</em>.</p>
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</div>
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<pre class="usage"><span class='fu'>mo_name</span>(<span class='kw'>x</span>, language = <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='kw'>...</span>)
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<pre class="usage"><span class='fu'>mo_name</span><span class='op'>(</span><span class='va'>x</span>, language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>, <span class='va'>...</span><span class='op'>)</span>
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<span class='fu'>mo_fullname</span>(<span class='kw'>x</span>, language = <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='kw'>...</span>)
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<span class='fu'>mo_fullname</span><span class='op'>(</span><span class='va'>x</span>, language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>, <span class='va'>...</span><span class='op'>)</span>
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<span class='fu'>mo_shortname</span>(<span class='kw'>x</span>, language = <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='kw'>...</span>)
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<span class='fu'>mo_shortname</span><span class='op'>(</span><span class='va'>x</span>, language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>, <span class='va'>...</span><span class='op'>)</span>
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<span class='fu'>mo_subspecies</span>(<span class='kw'>x</span>, language = <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='kw'>...</span>)
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<span class='fu'>mo_subspecies</span><span class='op'>(</span><span class='va'>x</span>, language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>, <span class='va'>...</span><span class='op'>)</span>
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<span class='fu'>mo_species</span>(<span class='kw'>x</span>, language = <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='kw'>...</span>)
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<span class='fu'>mo_species</span><span class='op'>(</span><span class='va'>x</span>, language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>, <span class='va'>...</span><span class='op'>)</span>
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<span class='fu'>mo_genus</span>(<span class='kw'>x</span>, language = <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='kw'>...</span>)
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<span class='fu'>mo_genus</span><span class='op'>(</span><span class='va'>x</span>, language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>, <span class='va'>...</span><span class='op'>)</span>
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<span class='fu'>mo_family</span>(<span class='kw'>x</span>, language = <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='kw'>...</span>)
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<span class='fu'>mo_family</span><span class='op'>(</span><span class='va'>x</span>, language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>, <span class='va'>...</span><span class='op'>)</span>
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<span class='fu'>mo_order</span>(<span class='kw'>x</span>, language = <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='kw'>...</span>)
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<span class='fu'>mo_order</span><span class='op'>(</span><span class='va'>x</span>, language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>, <span class='va'>...</span><span class='op'>)</span>
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<span class='fu'>mo_class</span>(<span class='kw'>x</span>, language = <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='kw'>...</span>)
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<span class='fu'>mo_class</span><span class='op'>(</span><span class='va'>x</span>, language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>, <span class='va'>...</span><span class='op'>)</span>
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<span class='fu'>mo_phylum</span>(<span class='kw'>x</span>, language = <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='kw'>...</span>)
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<span class='fu'>mo_phylum</span><span class='op'>(</span><span class='va'>x</span>, language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>, <span class='va'>...</span><span class='op'>)</span>
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<span class='fu'>mo_kingdom</span>(<span class='kw'>x</span>, language = <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='kw'>...</span>)
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<span class='fu'>mo_kingdom</span><span class='op'>(</span><span class='va'>x</span>, language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>, <span class='va'>...</span><span class='op'>)</span>
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<span class='fu'>mo_domain</span>(<span class='kw'>x</span>, language = <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='kw'>...</span>)
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<span class='fu'>mo_domain</span><span class='op'>(</span><span class='va'>x</span>, language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>, <span class='va'>...</span><span class='op'>)</span>
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<span class='fu'>mo_type</span>(<span class='kw'>x</span>, language = <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='kw'>...</span>)
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<span class='fu'>mo_type</span><span class='op'>(</span><span class='va'>x</span>, language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>, <span class='va'>...</span><span class='op'>)</span>
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<span class='fu'>mo_gramstain</span>(<span class='kw'>x</span>, language = <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='kw'>...</span>)
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<span class='fu'>mo_gramstain</span><span class='op'>(</span><span class='va'>x</span>, language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>, <span class='va'>...</span><span class='op'>)</span>
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<span class='fu'>mo_snomed</span>(<span class='kw'>x</span>, language = <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='kw'>...</span>)
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<span class='fu'>mo_snomed</span><span class='op'>(</span><span class='va'>x</span>, language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>, <span class='va'>...</span><span class='op'>)</span>
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<span class='fu'>mo_ref</span>(<span class='kw'>x</span>, language = <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='kw'>...</span>)
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<span class='fu'>mo_ref</span><span class='op'>(</span><span class='va'>x</span>, language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>, <span class='va'>...</span><span class='op'>)</span>
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<span class='fu'>mo_authors</span>(<span class='kw'>x</span>, language = <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='kw'>...</span>)
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<span class='fu'>mo_authors</span><span class='op'>(</span><span class='va'>x</span>, language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>, <span class='va'>...</span><span class='op'>)</span>
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<span class='fu'>mo_year</span>(<span class='kw'>x</span>, language = <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='kw'>...</span>)
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<span class='fu'>mo_year</span><span class='op'>(</span><span class='va'>x</span>, language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>, <span class='va'>...</span><span class='op'>)</span>
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<span class='fu'>mo_rank</span>(<span class='kw'>x</span>, language = <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='kw'>...</span>)
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<span class='fu'>mo_rank</span><span class='op'>(</span><span class='va'>x</span>, language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>, <span class='va'>...</span><span class='op'>)</span>
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<span class='fu'>mo_taxonomy</span>(<span class='kw'>x</span>, language = <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='kw'>...</span>)
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<span class='fu'>mo_taxonomy</span><span class='op'>(</span><span class='va'>x</span>, language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>, <span class='va'>...</span><span class='op'>)</span>
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<span class='fu'>mo_synonyms</span>(<span class='kw'>x</span>, language = <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='kw'>...</span>)
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<span class='fu'>mo_synonyms</span><span class='op'>(</span><span class='va'>x</span>, language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>, <span class='va'>...</span><span class='op'>)</span>
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<span class='fu'>mo_info</span>(<span class='kw'>x</span>, language = <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='kw'>...</span>)
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<span class='fu'>mo_info</span><span class='op'>(</span><span class='va'>x</span>, language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>, <span class='va'>...</span><span class='op'>)</span>
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<span class='fu'>mo_url</span>(<span class='kw'>x</span>, open = <span class='fl'>FALSE</span>, language = <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='kw'>...</span>)
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<span class='fu'>mo_url</span><span class='op'>(</span><span class='va'>x</span>, open <span class='op'>=</span> <span class='cn'>FALSE</span>, language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>, <span class='va'>...</span><span class='op'>)</span>
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<span class='fu'>mo_property</span>(<span class='kw'>x</span>, property = <span class='st'>"fullname"</span>, language = <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='kw'>...</span>)</pre>
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<span class='fu'>mo_property</span><span class='op'>(</span><span class='va'>x</span>, property <span class='op'>=</span> <span class='st'>"fullname"</span>, language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>, <span class='va'>...</span><span class='op'>)</span></pre>
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<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
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<table class="ref-arguments">
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@ -397,87 +397,87 @@ This package contains the complete taxonomic tree of almost all microorganisms (
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<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
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<pre class="examples"><span class='co'># taxonomic tree -----------------------------------------------------------</span>
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<span class='fu'>mo_kingdom</span>(<span class='st'>"E. coli"</span>) <span class='co'># "Bacteria"</span>
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<span class='fu'>mo_phylum</span>(<span class='st'>"E. coli"</span>) <span class='co'># "Proteobacteria"</span>
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<span class='fu'>mo_class</span>(<span class='st'>"E. coli"</span>) <span class='co'># "Gammaproteobacteria"</span>
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<span class='fu'>mo_order</span>(<span class='st'>"E. coli"</span>) <span class='co'># "Enterobacterales"</span>
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<span class='fu'>mo_family</span>(<span class='st'>"E. coli"</span>) <span class='co'># "Enterobacteriaceae"</span>
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<span class='fu'>mo_genus</span>(<span class='st'>"E. coli"</span>) <span class='co'># "Escherichia"</span>
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<span class='fu'>mo_species</span>(<span class='st'>"E. coli"</span>) <span class='co'># "coli"</span>
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<span class='fu'>mo_subspecies</span>(<span class='st'>"E. coli"</span>) <span class='co'># ""</span>
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<span class='fu'>mo_kingdom</span><span class='op'>(</span><span class='st'>"E. coli"</span><span class='op'>)</span> <span class='co'># "Bacteria"</span>
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<span class='fu'>mo_phylum</span><span class='op'>(</span><span class='st'>"E. coli"</span><span class='op'>)</span> <span class='co'># "Proteobacteria"</span>
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<span class='fu'>mo_class</span><span class='op'>(</span><span class='st'>"E. coli"</span><span class='op'>)</span> <span class='co'># "Gammaproteobacteria"</span>
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<span class='fu'>mo_order</span><span class='op'>(</span><span class='st'>"E. coli"</span><span class='op'>)</span> <span class='co'># "Enterobacterales"</span>
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<span class='fu'>mo_family</span><span class='op'>(</span><span class='st'>"E. coli"</span><span class='op'>)</span> <span class='co'># "Enterobacteriaceae"</span>
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<span class='fu'>mo_genus</span><span class='op'>(</span><span class='st'>"E. coli"</span><span class='op'>)</span> <span class='co'># "Escherichia"</span>
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<span class='fu'>mo_species</span><span class='op'>(</span><span class='st'>"E. coli"</span><span class='op'>)</span> <span class='co'># "coli"</span>
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<span class='fu'>mo_subspecies</span><span class='op'>(</span><span class='st'>"E. coli"</span><span class='op'>)</span> <span class='co'># ""</span>
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<span class='co'># colloquial properties ----------------------------------------------------</span>
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<span class='fu'>mo_name</span>(<span class='st'>"E. coli"</span>) <span class='co'># "Escherichia coli"</span>
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<span class='fu'>mo_fullname</span>(<span class='st'>"E. coli"</span>) <span class='co'># "Escherichia coli" - same as mo_name()</span>
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<span class='fu'>mo_shortname</span>(<span class='st'>"E. coli"</span>) <span class='co'># "E. coli"</span>
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<span class='fu'>mo_name</span><span class='op'>(</span><span class='st'>"E. coli"</span><span class='op'>)</span> <span class='co'># "Escherichia coli"</span>
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<span class='fu'>mo_fullname</span><span class='op'>(</span><span class='st'>"E. coli"</span><span class='op'>)</span> <span class='co'># "Escherichia coli" - same as mo_name()</span>
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<span class='fu'>mo_shortname</span><span class='op'>(</span><span class='st'>"E. coli"</span><span class='op'>)</span> <span class='co'># "E. coli"</span>
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<span class='co'># other properties ---------------------------------------------------------</span>
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<span class='fu'>mo_gramstain</span>(<span class='st'>"E. coli"</span>) <span class='co'># "Gram-negative"</span>
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<span class='fu'>mo_snomed</span>(<span class='st'>"E. coli"</span>) <span class='co'># 112283007, 116395006, ... (SNOMED codes)</span>
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<span class='fu'>mo_type</span>(<span class='st'>"E. coli"</span>) <span class='co'># "Bacteria" (equal to kingdom, but may be translated)</span>
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<span class='fu'>mo_rank</span>(<span class='st'>"E. coli"</span>) <span class='co'># "species"</span>
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<span class='fu'>mo_url</span>(<span class='st'>"E. coli"</span>) <span class='co'># get the direct url to the online database entry</span>
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<span class='fu'>mo_synonyms</span>(<span class='st'>"E. coli"</span>) <span class='co'># get previously accepted taxonomic names</span>
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<span class='fu'>mo_gramstain</span><span class='op'>(</span><span class='st'>"E. coli"</span><span class='op'>)</span> <span class='co'># "Gram-negative"</span>
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<span class='fu'>mo_snomed</span><span class='op'>(</span><span class='st'>"E. coli"</span><span class='op'>)</span> <span class='co'># 112283007, 116395006, ... (SNOMED codes)</span>
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<span class='fu'>mo_type</span><span class='op'>(</span><span class='st'>"E. coli"</span><span class='op'>)</span> <span class='co'># "Bacteria" (equal to kingdom, but may be translated)</span>
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<span class='fu'>mo_rank</span><span class='op'>(</span><span class='st'>"E. coli"</span><span class='op'>)</span> <span class='co'># "species"</span>
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<span class='fu'>mo_url</span><span class='op'>(</span><span class='st'>"E. coli"</span><span class='op'>)</span> <span class='co'># get the direct url to the online database entry</span>
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<span class='fu'>mo_synonyms</span><span class='op'>(</span><span class='st'>"E. coli"</span><span class='op'>)</span> <span class='co'># get previously accepted taxonomic names</span>
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<span class='co'># scientific reference -----------------------------------------------------</span>
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<span class='fu'>mo_ref</span>(<span class='st'>"E. coli"</span>) <span class='co'># "Castellani et al., 1919"</span>
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<span class='fu'>mo_authors</span>(<span class='st'>"E. coli"</span>) <span class='co'># "Castellani et al."</span>
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<span class='fu'>mo_year</span>(<span class='st'>"E. coli"</span>) <span class='co'># 1919</span>
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<span class='fu'>mo_ref</span><span class='op'>(</span><span class='st'>"E. coli"</span><span class='op'>)</span> <span class='co'># "Castellani et al., 1919"</span>
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<span class='fu'>mo_authors</span><span class='op'>(</span><span class='st'>"E. coli"</span><span class='op'>)</span> <span class='co'># "Castellani et al."</span>
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<span class='fu'>mo_year</span><span class='op'>(</span><span class='st'>"E. coli"</span><span class='op'>)</span> <span class='co'># 1919</span>
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<span class='co'># abbreviations known in the field -----------------------------------------</span>
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<span class='fu'>mo_genus</span>(<span class='st'>"MRSA"</span>) <span class='co'># "Staphylococcus"</span>
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<span class='fu'>mo_species</span>(<span class='st'>"MRSA"</span>) <span class='co'># "aureus"</span>
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<span class='fu'>mo_shortname</span>(<span class='st'>"VISA"</span>) <span class='co'># "S. aureus"</span>
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<span class='fu'>mo_gramstain</span>(<span class='st'>"VISA"</span>) <span class='co'># "Gram-positive"</span>
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<span class='fu'>mo_genus</span><span class='op'>(</span><span class='st'>"MRSA"</span><span class='op'>)</span> <span class='co'># "Staphylococcus"</span>
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<span class='fu'>mo_species</span><span class='op'>(</span><span class='st'>"MRSA"</span><span class='op'>)</span> <span class='co'># "aureus"</span>
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<span class='fu'>mo_shortname</span><span class='op'>(</span><span class='st'>"VISA"</span><span class='op'>)</span> <span class='co'># "S. aureus"</span>
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<span class='fu'>mo_gramstain</span><span class='op'>(</span><span class='st'>"VISA"</span><span class='op'>)</span> <span class='co'># "Gram-positive"</span>
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<span class='fu'>mo_genus</span>(<span class='st'>"EHEC"</span>) <span class='co'># "Escherichia"</span>
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<span class='fu'>mo_species</span>(<span class='st'>"EHEC"</span>) <span class='co'># "coli"</span>
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<span class='fu'>mo_genus</span><span class='op'>(</span><span class='st'>"EHEC"</span><span class='op'>)</span> <span class='co'># "Escherichia"</span>
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<span class='fu'>mo_species</span><span class='op'>(</span><span class='st'>"EHEC"</span><span class='op'>)</span> <span class='co'># "coli"</span>
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<span class='co'># known subspecies ---------------------------------------------------------</span>
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<span class='fu'>mo_name</span>(<span class='st'>"doylei"</span>) <span class='co'># "Campylobacter jejuni doylei"</span>
|
||||
<span class='fu'>mo_genus</span>(<span class='st'>"doylei"</span>) <span class='co'># "Campylobacter"</span>
|
||||
<span class='fu'>mo_species</span>(<span class='st'>"doylei"</span>) <span class='co'># "jejuni"</span>
|
||||
<span class='fu'>mo_subspecies</span>(<span class='st'>"doylei"</span>) <span class='co'># "doylei"</span>
|
||||
<span class='fu'>mo_name</span><span class='op'>(</span><span class='st'>"doylei"</span><span class='op'>)</span> <span class='co'># "Campylobacter jejuni doylei"</span>
|
||||
<span class='fu'>mo_genus</span><span class='op'>(</span><span class='st'>"doylei"</span><span class='op'>)</span> <span class='co'># "Campylobacter"</span>
|
||||
<span class='fu'>mo_species</span><span class='op'>(</span><span class='st'>"doylei"</span><span class='op'>)</span> <span class='co'># "jejuni"</span>
|
||||
<span class='fu'>mo_subspecies</span><span class='op'>(</span><span class='st'>"doylei"</span><span class='op'>)</span> <span class='co'># "doylei"</span>
|
||||
|
||||
<span class='fu'>mo_fullname</span>(<span class='st'>"K. pneu rh"</span>) <span class='co'># "Klebsiella pneumoniae rhinoscleromatis"</span>
|
||||
<span class='fu'>mo_shortname</span>(<span class='st'>"K. pneu rh"</span>) <span class='co'># "K. pneumoniae"</span>
|
||||
<span class='fu'>mo_fullname</span><span class='op'>(</span><span class='st'>"K. pneu rh"</span><span class='op'>)</span> <span class='co'># "Klebsiella pneumoniae rhinoscleromatis"</span>
|
||||
<span class='fu'>mo_shortname</span><span class='op'>(</span><span class='st'>"K. pneu rh"</span><span class='op'>)</span> <span class='co'># "K. pneumoniae"</span>
|
||||
|
||||
<span class='co'># \donttest{</span>
|
||||
<span class='co'># Becker classification, see ?as.mo ----------------------------------------</span>
|
||||
<span class='fu'>mo_fullname</span>(<span class='st'>"S. epi"</span>) <span class='co'># "Staphylococcus epidermidis"</span>
|
||||
<span class='fu'>mo_fullname</span>(<span class='st'>"S. epi"</span>, Becker = <span class='fl'>TRUE</span>) <span class='co'># "Coagulase-negative Staphylococcus (CoNS)"</span>
|
||||
<span class='fu'>mo_shortname</span>(<span class='st'>"S. epi"</span>) <span class='co'># "S. epidermidis"</span>
|
||||
<span class='fu'>mo_shortname</span>(<span class='st'>"S. epi"</span>, Becker = <span class='fl'>TRUE</span>) <span class='co'># "CoNS"</span>
|
||||
<span class='fu'>mo_fullname</span><span class='op'>(</span><span class='st'>"S. epi"</span><span class='op'>)</span> <span class='co'># "Staphylococcus epidermidis"</span>
|
||||
<span class='fu'>mo_fullname</span><span class='op'>(</span><span class='st'>"S. epi"</span>, Becker <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> <span class='co'># "Coagulase-negative Staphylococcus (CoNS)"</span>
|
||||
<span class='fu'>mo_shortname</span><span class='op'>(</span><span class='st'>"S. epi"</span><span class='op'>)</span> <span class='co'># "S. epidermidis"</span>
|
||||
<span class='fu'>mo_shortname</span><span class='op'>(</span><span class='st'>"S. epi"</span>, Becker <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> <span class='co'># "CoNS"</span>
|
||||
|
||||
<span class='co'># Lancefield classification, see ?as.mo ------------------------------------</span>
|
||||
<span class='fu'>mo_fullname</span>(<span class='st'>"S. pyo"</span>) <span class='co'># "Streptococcus pyogenes"</span>
|
||||
<span class='fu'>mo_fullname</span>(<span class='st'>"S. pyo"</span>, Lancefield = <span class='fl'>TRUE</span>) <span class='co'># "Streptococcus group A"</span>
|
||||
<span class='fu'>mo_shortname</span>(<span class='st'>"S. pyo"</span>) <span class='co'># "S. pyogenes"</span>
|
||||
<span class='fu'>mo_shortname</span>(<span class='st'>"S. pyo"</span>, Lancefield = <span class='fl'>TRUE</span>) <span class='co'># "GAS" (='Group A Streptococci')</span>
|
||||
<span class='fu'>mo_fullname</span><span class='op'>(</span><span class='st'>"S. pyo"</span><span class='op'>)</span> <span class='co'># "Streptococcus pyogenes"</span>
|
||||
<span class='fu'>mo_fullname</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'># "Streptococcus group A"</span>
|
||||
<span class='fu'>mo_shortname</span><span class='op'>(</span><span class='st'>"S. pyo"</span><span class='op'>)</span> <span class='co'># "S. pyogenes"</span>
|
||||
<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='fu'>mo_gramstain</span>(<span class='st'>"E. coli"</span>, language = <span class='st'>"de"</span>) <span class='co'># "Gramnegativ"</span>
|
||||
<span class='fu'>mo_gramstain</span>(<span class='st'>"E. coli"</span>, language = <span class='st'>"nl"</span>) <span class='co'># "Gram-negatief"</span>
|
||||
<span class='fu'>mo_gramstain</span>(<span class='st'>"E. coli"</span>, language = <span class='st'>"es"</span>) <span class='co'># "Gram negativo"</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>
|
||||
|
||||
<span class='co'># mo_type is equal to mo_kingdom, but mo_kingdom will remain official</span>
|
||||
<span class='fu'>mo_kingdom</span>(<span class='st'>"E. coli"</span>) <span class='co'># "Bacteria" on a German system</span>
|
||||
<span class='fu'>mo_type</span>(<span class='st'>"E. coli"</span>) <span class='co'># "Bakterien" on a German system</span>
|
||||
<span class='fu'>mo_type</span>(<span class='st'>"E. coli"</span>) <span class='co'># "Bacteria" on an English system</span>
|
||||
<span class='fu'>mo_kingdom</span><span class='op'>(</span><span class='st'>"E. coli"</span><span class='op'>)</span> <span class='co'># "Bacteria" on a German system</span>
|
||||
<span class='fu'>mo_type</span><span class='op'>(</span><span class='st'>"E. coli"</span><span class='op'>)</span> <span class='co'># "Bakterien" on a German system</span>
|
||||
<span class='fu'>mo_type</span><span class='op'>(</span><span class='st'>"E. coli"</span><span class='op'>)</span> <span class='co'># "Bacteria" on an English system</span>
|
||||
|
||||
<span class='fu'>mo_fullname</span>(<span class='st'>"S. pyogenes"</span>,
|
||||
Lancefield = <span class='fl'>TRUE</span>,
|
||||
language = <span class='st'>"de"</span>) <span class='co'># "Streptococcus Gruppe A"</span>
|
||||
<span class='fu'>mo_fullname</span>(<span class='st'>"S. pyogenes"</span>,
|
||||
Lancefield = <span class='fl'>TRUE</span>,
|
||||
language = <span class='st'>"nl"</span>) <span class='co'># "Streptococcus groep A"</span>
|
||||
<span class='fu'>mo_fullname</span><span class='op'>(</span><span class='st'>"S. pyogenes"</span>,
|
||||
Lancefield <span class='op'>=</span> <span class='cn'>TRUE</span>,
|
||||
language <span class='op'>=</span> <span class='st'>"de"</span><span class='op'>)</span> <span class='co'># "Streptococcus Gruppe A"</span>
|
||||
<span class='fu'>mo_fullname</span><span class='op'>(</span><span class='st'>"S. pyogenes"</span>,
|
||||
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'># get a list with the complete taxonomy (from kingdom to subspecies)</span>
|
||||
<span class='fu'>mo_taxonomy</span>(<span class='st'>"E. coli"</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>
|
||||
<span class='fu'>mo_info</span>(<span class='st'>"E. coli"</span>)
|
||||
<span class='fu'>mo_info</span><span class='op'>(</span><span class='st'>"E. coli"</span><span class='op'>)</span>
|
||||
<span class='co'># }</span>
|
||||
</pre>
|
||||
</div>
|
||||
@ -495,7 +495,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
Reference in New Issue
Block a user