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(v0.8.0.9036) complete documentation rewrite
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<script src="../extra.js"></script>
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<meta property="og:title" content="Property of a microorganism — mo_property" />
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<meta property="og:description" content="Use these functions to return a specific property of a microorganism. All input values will be evaluated internally with as.mo, which makes it possible for input of these functions to use microbial abbreviations, codes and names. See Examples." />
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<meta property="og:description" content="Use these functions to return a specific property of a microorganism. All input values will be evaluated internally with as.mo(), which makes it possible for input of these functions to use microbial abbreviations, codes and names. See Examples." />
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<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.png" />
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<meta name="twitter:card" content="summary" />
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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">0.8.0.9035</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9036</span>
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</span>
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</div>
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</div>
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<div class="ref-description">
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<p>Use these functions to return a specific property of a microorganism. All input values will be evaluated internally with <code><a href='as.mo.html'>as.mo</a></code>, which makes it possible for input of these functions to use microbial abbreviations, codes and names. See Examples.</p>
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<p>Use these functions to return a specific property of a microorganism. All input values will be evaluated internally with <code><a href='as.mo.html'>as.mo()</a></code>, which makes it possible for input of these functions to use microbial abbreviations, codes and names. See Examples.</p>
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</div>
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<pre class="usage"><span class='fu'>mo_name</span>(<span class='no'>x</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='no'>...</span>)
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<colgroup><col class="name" /><col class="desc" /></colgroup>
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<tr>
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<th>x</th>
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<td><p>any (vector of) text that can be coerced to a valid microorganism code with <code><a href='as.mo.html'>as.mo</a></code></p></td>
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<td><p>any (vector of) text that can be coerced to a valid microorganism code with <code><a href='as.mo.html'>as.mo()</a></code></p></td>
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</tr>
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<tr>
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<th>language</th>
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<td><p>language of the returned text, defaults to system language (see <code><a href='translate.html'>get_locale</a></code>) and can also be set with <code><a href='https://rdrr.io/r/base/options.html'>getOption</a>("AMR_locale")</code>. Use <code>language = NULL</code> or <code>language = ""</code> to prevent translation.</p></td>
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<td><p>language of the returned text, defaults to system language (see <code><a href='translate.html'>get_locale()</a></code>) and can also be set with <code><a href='https://rdrr.io/r/base/options.html'>getOption("AMR_locale")</a></code>. Use <code>language = NULL</code> or <code>language = ""</code> to prevent translation.</p></td>
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</tr>
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<tr>
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<th>...</th>
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<td><p>other parameters passed on to <code><a href='as.mo.html'>as.mo</a></code></p></td>
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<td><p>other parameters passed on to <code><a href='as.mo.html'>as.mo()</a></code></p></td>
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</tr>
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<tr>
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<th>open</th>
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<td><p>browse the URL using <code><a href='https://rdrr.io/r/utils/browseURL.html'>browseURL</a>()</code></p></td>
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<td><p>browse the URL using <code><a href='https://rdrr.io/r/utils/browseURL.html'>utils::browseURL()</a></code></p></td>
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</tr>
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<tr>
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<th>property</th>
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<td><p>one of the column names of the <code><a href='microorganisms.html'>microorganisms</a></code> data set or <code>"shortname"</code></p></td>
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<td><p>one of the column names of the <a href='microorganisms.html'>microorganisms</a> data set or <code>"shortname"</code></p></td>
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</tr>
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</table>
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<ul>
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<li><p>An <code>integer</code> in case of <code>mo_year</code></p></li>
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<li><p>A <code>list</code> in case of <code>mo_taxonomy</code></p></li>
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<li><p>A named <code>character</code> in case of <code>mo_url</code></p></li>
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<li><p>A <code>character</code> in all other cases</p></li>
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<li><p>An <code><a href='https://rdrr.io/r/base/integer.html'>integer</a></code> in case of <code>mo_year()</code></p></li>
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<li><p>A <code><a href='https://rdrr.io/r/base/list.html'>list</a></code> in case of <code>mo_taxonomy()</code></p></li>
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<li><p>A named <code><a href='https://rdrr.io/r/base/character.html'>character</a></code> in case of <code>mo_url()</code></p></li>
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<li><p>A <code><a href='https://rdrr.io/r/base/character.html'>character</a></code> in all other cases</p></li>
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</ul>
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<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
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<p>All functions will return the most recently known taxonomic property according to the Catalogue of Life, except for <code>mo_ref</code>, <code>mo_authors</code> and <code>mo_year</code>. This leads to the following results:</p><ul>
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<p>All functions will return the most recently known taxonomic property according to the Catalogue of Life, except for <code>mo_ref()</code>, <code>mo_authors()</code> and <code>mo_year()</code>. This leads to the following results:</p><ul>
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<li><p><code>mo_name("Chlamydia psittaci")</code> will return <code>"Chlamydophila psittaci"</code> (with a warning about the renaming)</p></li>
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<li><p><code>mo_ref("Chlamydia psittaci")</code> will return <code>"Page, 1968"</code> (with a warning about the renaming)</p></li>
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<li><p><code>mo_ref("Chlamydophila psittaci")</code> will return <code>"Everett et al., 1999"</code> (without a warning)</p></li>
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<p><img src='figures/logo_col.png' height=40px style=margin-bottom:5px /> <br />
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This package contains the complete taxonomic tree of almost all microorganisms (~70,000 species) from the authoritative and comprehensive Catalogue of Life (<a href='http://www.catalogueoflife.org'>http://www.catalogueoflife.org</a>). The Catalogue of Life is the most comprehensive and authoritative global index of species currently available.</p>
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<p><a href='catalogue_of_life.html'>Click here</a> for more information about the included taxa. Check which version of the Catalogue of Life was included in this package with <code><a href='catalogue_of_life_version.html'>catalogue_of_life_version</a>()</code>.</p>
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<p><a href='catalogue_of_life.html'>Click here</a> for more information about the included taxa. Check which version of the Catalogue of Life was included in this package with <code><a href='catalogue_of_life_version.html'>catalogue_of_life_version()</a></code>.</p>
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<h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>
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<p>[1] Becker K <em>et al.</em> <strong>Coagulase-Negative Staphylococci</strong>. 2014. Clin Microbiol Rev. 27(4): 870–926. <a href='https://dx.doi.org/10.1128/CMR.00109-13'>https://dx.doi.org/10.1128/CMR.00109-13</a></p>
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<p>[2] Becker K <em>et al.</em> <strong>Implications of identifying the recently defined members of the <em>S. aureus</em> complex, <em>S. argenteus</em> and <em>S. schweitzeri</em>: A position paper of members of the ESCMID Study Group for staphylococci and Staphylococcal Diseases (ESGS).</strong> 2019. Clin Microbiol Infect. <a href='https://doi.org/10.1016/j.cmi.2019.02.028'>https://doi.org/10.1016/j.cmi.2019.02.028</a></p>
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<p>[3] Lancefield RC <strong>A serological differentiation of human and other groups of hemolytic streptococci</strong>. 1933. J Exp Med. 57(4): 571–95. <a href='https://dx.doi.org/10.1084/jem.57.4.571'>https://dx.doi.org/10.1084/jem.57.4.571</a></p>
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<p>[4] Catalogue of Life: Annual Checklist (public online taxonomic database), <a href='http://www.catalogueoflife.org'>http://www.catalogueoflife.org</a> (check included annual version with <code><a href='catalogue_of_life_version.html'>catalogue_of_life_version</a>()</code>).</p>
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<ol>
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<li><p>Becker K <em>et al.</em> <strong>Coagulase-Negative Staphylococci</strong>. 2014. Clin Microbiol Rev. 27(4): 870–926. <a href='https://dx.doi.org/10.1128/CMR.00109-13'>https://dx.doi.org/10.1128/CMR.00109-13</a></p></li>
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<li><p>Becker K <em>et al.</em> <strong>Implications of identifying the recently defined members of the <em>S. aureus</em> complex, <em>S. argenteus</em> and <em>S. schweitzeri</em>: A position paper of members of the ESCMID Study Group for staphylococci and Staphylococcal Diseases (ESGS).</strong> 2019. Clin Microbiol Infect. <a href='https://doi.org/10.1016/j.cmi.2019.02.028'>https://doi.org/10.1016/j.cmi.2019.02.028</a></p></li>
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<li><p>Lancefield RC <strong>A serological differentiation of human and other groups of hemolytic streptococci</strong>. 1933. J Exp Med. 57(4): 571–95. <a href='https://dx.doi.org/10.1084/jem.57.4.571'>https://dx.doi.org/10.1084/jem.57.4.571</a></p></li>
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<li><p>Catalogue of Life: Annual Checklist (public online taxonomic database), <a href='http://www.catalogueoflife.org'>http://www.catalogueoflife.org</a> (check included annual version with <code><a href='catalogue_of_life_version.html'>catalogue_of_life_version()</a></code>).</p></li>
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</ol>
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<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>
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@ -349,7 +352,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
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<p>On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
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<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
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<div class='dont-index'><p><code><a href='microorganisms.html'>microorganisms</a></code></p></div>
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<div class='dont-index'><p><a href='microorganisms.html'>microorganisms</a></p></div>
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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='co'># get a list with the complete taxonomy (from kingdom to subspecies)</span>
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<span class='fu'>mo_taxonomy</span>(<span class='st'>"E. coli"</span>)
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<span class='co'># get a list with the taxonomy, the authors and the URL to the online database</span>
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<span class='co'># get a list with the taxonomy, the authors, Gram-stain and URL to the online database</span>
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<span class='fu'>mo_info</span>(<span class='st'>"E. coli"</span>)
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<span class='co'># }</span></pre>
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</div>
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