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(v1.8.1.9014) add Toxoplasma
This commit is contained in:
@ -17,7 +17,7 @@
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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="Released version">1.8.1.9011</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9014</span>
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</span>
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</div>
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@ -162,53 +162,76 @@
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</div>
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<div id="ref-usage">
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<div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">as.mo</span><span class="op">(</span>
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<span class="va">x</span>,
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Becker <span class="op">=</span> <span class="cn">FALSE</span>,
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Lancefield <span class="op">=</span> <span class="cn">FALSE</span>,
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allow_uncertain <span class="op">=</span> <span class="cn">TRUE</span>,
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reference_df <span class="op">=</span> <span class="fu"><a href="mo_source.html">get_mo_source</a></span><span class="op">(</span><span class="op">)</span>,
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||||
ignore_pattern <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_ignore_pattern"</span><span class="op">)</span>,
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language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,
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info <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/interactive.html" class="external-link">interactive</a></span><span class="op">(</span><span class="op">)</span>,
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<span class="va">...</span>
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<span class="op">)</span>
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||||
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||||
<span class="fu">is.mo</span><span class="op">(</span><span class="va">x</span><span class="op">)</span>
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<span class="fu">mo_failures</span><span class="op">(</span><span class="op">)</span>
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<span class="fu">mo_uncertainties</span><span class="op">(</span><span class="op">)</span>
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<span class="fu">mo_renamed</span><span class="op">(</span><span class="op">)</span></code></pre></div>
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<div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">as.mo</span><span class="op">(</span></span>
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<span> <span class="va">x</span>,</span>
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<span> Becker <span class="op">=</span> <span class="cn">FALSE</span>,</span>
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<span> Lancefield <span class="op">=</span> <span class="cn">FALSE</span>,</span>
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<span> allow_uncertain <span class="op">=</span> <span class="cn">TRUE</span>,</span>
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<span> reference_df <span class="op">=</span> <span class="fu"><a href="mo_source.html">get_mo_source</a></span><span class="op">(</span><span class="op">)</span>,</span>
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<span> ignore_pattern <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_ignore_pattern"</span><span class="op">)</span>,</span>
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<span> language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,</span>
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<span> info <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/interactive.html" class="external-link">interactive</a></span><span class="op">(</span><span class="op">)</span>,</span>
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<span> <span class="va">...</span></span>
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<span><span class="op">)</span></span>
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<span></span>
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<span><span class="fu">is.mo</span><span class="op">(</span><span class="va">x</span><span class="op">)</span></span>
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<span></span>
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<span><span class="fu">mo_failures</span><span class="op">(</span><span class="op">)</span></span>
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||||
<span></span>
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||||
<span><span class="fu">mo_uncertainties</span><span class="op">(</span><span class="op">)</span></span>
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<span></span>
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<span><span class="fu">mo_renamed</span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
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</div>
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<div id="arguments">
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<h2>Arguments</h2>
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<dl><dt>x</dt>
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<dd><p>a <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> vector or a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> with one or two columns</p></dd>
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<dt>Becker</dt>
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<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> 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>
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<p>This excludes <em>Staphylococcus aureus</em> at default, use <code>Becker = "all"</code> to also categorise <em>S. aureus</em> as "CoPS".</p></dd>
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||||
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||||
<dt>Lancefield</dt>
|
||||
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether a beta-haemolytic <em>Streptococcus</em> should be categorised into Lancefield groups instead of their own species, according to Rebecca C. Lancefield (4). These streptococci will be categorised in their first group, e.g. <em>Streptococcus dysgalactiae</em> will be group C, although officially it was also categorised into groups G and L.</p>
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||||
<p>This excludes enterococci at default (who are in group D), use <code>Lancefield = "all"</code> to also categorise all enterococci as group D.</p></dd>
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<dt>allow_uncertain</dt>
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<dd><p>a number between <code>0</code> (or <code>"none"</code>) and <code>3</code> (or <code>"all"</code>), or <code>TRUE</code> (= <code>2</code>) or <code>FALSE</code> (= <code>0</code>) to indicate whether the input should be checked for less probable results, see <em>Details</em></p></dd>
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<dt>reference_df</dt>
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||||
<dd><p>a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> to be used for extra reference when translating <code>x</code> to a valid <code>mo</code>. See <code><a href="mo_source.html">set_mo_source()</a></code> and <code><a href="mo_source.html">get_mo_source()</a></code> to automate the usage of your own codes (e.g. used in your analysis or organisation).</p></dd>
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<dt>ignore_pattern</dt>
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<dd><p>a regular expression (case-insensitive) of which all matches in <code>x</code> must return <code>NA</code>. This can be convenient to exclude known non-relevant input and can also be set with the option <code>AMR_ignore_pattern</code>, e.g. <code>options(AMR_ignore_pattern = "(not reported|contaminated flora)")</code>.</p></dd>
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<dt>language</dt>
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<dd><p>language to translate text like "no growth", which defaults to the system language (see <code><a href="translate.html">get_AMR_locale()</a></code>)</p></dd>
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<dt>info</dt>
|
||||
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate if a progress bar should be printed if more than 25 items are to be coerced, defaults to <code>TRUE</code> only in interactive mode</p></dd>
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||||
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<dt>...</dt>
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||||
<dd><p>other arguments passed on to functions</p></dd>
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||||
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||||
</dl></div>
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||||
<div id="value">
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||||
<h2>Value</h2>
|
||||
<p>A <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a><a href="https://rdrr.io/r/base/vector.html" class="external-link">vector</a> with additional class <code>mo</code></p>
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||||
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||||
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||||
<p>A <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a></p>
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||||
<p></p>
|
||||
<p><a href="https://rdrr.io/r/base/vector.html" class="external-link">vector</a> with additional class <code>mo</code></p>
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||||
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</div>
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<div id="details">
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<h2>Details</h2>
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@ -218,7 +241,18 @@
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<p>A microorganism (MO) code from this package (class: <code>mo</code>) is human readable and typically looks like these examples:</p>
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<p></p><div class="sourceCode"><pre><code></code></pre><p></p></div>
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<p></p><div class="sourceCode"><pre><code><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a> Code Full name</span>
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<span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a> <span class="sc">---------------</span> <span class="sc">--------------------------------------</span></span>
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<span id="cb1-3"><a href="#cb1-3" aria-hidden="true" tabindex="-1"></a> B_KLBSL Klebsiella</span>
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<span id="cb1-4"><a href="#cb1-4" aria-hidden="true" tabindex="-1"></a> B_KLBSL_PNMN Klebsiella pneumoniae</span>
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<span id="cb1-5"><a href="#cb1-5" aria-hidden="true" tabindex="-1"></a> B_KLBSL_PNMN_RHNS Klebsiella pneumoniae rhinoscleromatis</span>
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<span id="cb1-6"><a href="#cb1-6" aria-hidden="true" tabindex="-1"></a> <span class="sc">|</span> <span class="er">|</span> <span class="er">|</span> <span class="er">|</span></span>
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||||
<span id="cb1-7"><a href="#cb1-7" aria-hidden="true" tabindex="-1"></a> <span class="er">|</span> <span class="er">|</span> <span class="er">|</span> <span class="er">|</span></span>
|
||||
<span id="cb1-8"><a href="#cb1-8" aria-hidden="true" tabindex="-1"></a> <span class="er">|</span> <span class="er">|</span> <span class="er">|</span> \<span class="sc">--</span><span class="ot">-></span> subspecies, a <span class="dv">4-5</span> letter acronym</span>
|
||||
<span id="cb1-9"><a href="#cb1-9" aria-hidden="true" tabindex="-1"></a> <span class="sc">|</span> <span class="er">|</span> \<span class="sc">---</span><span class="ot">-></span> species, a <span class="dv">4-5</span> letter acronym</span>
|
||||
<span id="cb1-10"><a href="#cb1-10" aria-hidden="true" tabindex="-1"></a> <span class="sc">|</span> \<span class="sc">---</span><span class="ot">-></span> genus, a <span class="dv">5-7</span> letter acronym</span>
|
||||
<span id="cb1-11"><a href="#cb1-11" aria-hidden="true" tabindex="-1"></a> \<span class="sc">---</span><span class="ot">-></span> taxonomic kingdom<span class="sc">:</span> <span class="fu">A</span> (Archaea), <span class="fu">AN</span> (Animalia), <span class="fu">B</span> (Bacteria),</span>
|
||||
<span id="cb1-12"><a href="#cb1-12" aria-hidden="true" tabindex="-1"></a> <span class="fu">C</span> (Chromista), <span class="fu">F</span> (Fungi), <span class="fu">P</span> (Protozoa)</span></code></pre><p></p></div>
|
||||
<p>Values that cannot be coerced will be considered 'unknown' and will get the MO code <code>UNKNOWN</code>.</p>
|
||||
<p>Use the <code><a href="mo_property.html">mo_*</a></code> functions to get properties based on the returned code, see <em>Examples</em>.</p>
|
||||
<p>The algorithm uses data from the Catalogue of Life (see below) and from one other source (see <a href="microorganisms.html">microorganisms</a>).</p>
|
||||
@ -318,44 +352,43 @@ This package contains the complete taxonomic tree of almost all microorganisms (
|
||||
|
||||
<div id="ref-examples">
|
||||
<h2>Examples</h2>
|
||||
<div class="sourceCode"><pre class="sourceCode r"><code><span class="co"># \donttest{</span>
|
||||
<span class="co"># These examples all return "B_STPHY_AURS", the ID of S. aureus:</span>
|
||||
<span class="fu">as.mo</span><span class="op">(</span><span class="st">"sau"</span><span class="op">)</span> <span class="co"># WHONET code</span>
|
||||
<span class="fu">as.mo</span><span class="op">(</span><span class="st">"stau"</span><span class="op">)</span>
|
||||
<span class="fu">as.mo</span><span class="op">(</span><span class="st">"STAU"</span><span class="op">)</span>
|
||||
<span class="fu">as.mo</span><span class="op">(</span><span class="st">"staaur"</span><span class="op">)</span>
|
||||
<span class="fu">as.mo</span><span class="op">(</span><span class="st">"S. aureus"</span><span class="op">)</span>
|
||||
<span class="fu">as.mo</span><span class="op">(</span><span class="st">"S aureus"</span><span class="op">)</span>
|
||||
<span class="fu">as.mo</span><span class="op">(</span><span class="st">"Staphylococcus aureus"</span><span class="op">)</span>
|
||||
<span class="fu">as.mo</span><span class="op">(</span><span class="st">"Staphylococcus aureus (MRSA)"</span><span class="op">)</span>
|
||||
<span class="fu">as.mo</span><span class="op">(</span><span class="st">"Zthafilokkoockus oureuz"</span><span class="op">)</span> <span class="co"># handles incorrect spelling</span>
|
||||
<span class="fu">as.mo</span><span class="op">(</span><span class="st">"MRSA"</span><span class="op">)</span> <span class="co"># Methicillin Resistant S. aureus</span>
|
||||
<span class="fu">as.mo</span><span class="op">(</span><span class="st">"VISA"</span><span class="op">)</span> <span class="co"># Vancomycin Intermediate S. aureus</span>
|
||||
<span class="fu">as.mo</span><span class="op">(</span><span class="st">"VRSA"</span><span class="op">)</span> <span class="co"># Vancomycin Resistant S. aureus</span>
|
||||
<span class="fu">as.mo</span><span class="op">(</span><span class="fl">115329001</span><span class="op">)</span> <span class="co"># SNOMED CT code</span>
|
||||
|
||||
<span class="co"># Dyslexia is no problem - these all work:</span>
|
||||
<span class="fu">as.mo</span><span class="op">(</span><span class="st">"Ureaplasma urealyticum"</span><span class="op">)</span>
|
||||
<span class="fu">as.mo</span><span class="op">(</span><span class="st">"Ureaplasma urealyticus"</span><span class="op">)</span>
|
||||
<span class="fu">as.mo</span><span class="op">(</span><span class="st">"Ureaplasmium urealytica"</span><span class="op">)</span>
|
||||
<span class="fu">as.mo</span><span class="op">(</span><span class="st">"Ureaplazma urealitycium"</span><span class="op">)</span>
|
||||
|
||||
<span class="fu">as.mo</span><span class="op">(</span><span class="st">"Streptococcus group A"</span><span class="op">)</span>
|
||||
<span class="fu">as.mo</span><span class="op">(</span><span class="st">"GAS"</span><span class="op">)</span> <span class="co"># Group A Streptococci</span>
|
||||
<span class="fu">as.mo</span><span class="op">(</span><span class="st">"GBS"</span><span class="op">)</span> <span class="co"># Group B Streptococci</span>
|
||||
|
||||
<span class="fu">as.mo</span><span class="op">(</span><span class="st">"S. epidermidis"</span><span class="op">)</span> <span class="co"># will remain species: B_STPHY_EPDR</span>
|
||||
<span class="fu">as.mo</span><span class="op">(</span><span class="st">"S. epidermidis"</span>, Becker <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span> <span class="co"># will not remain species: B_STPHY_CONS</span>
|
||||
|
||||
<span class="fu">as.mo</span><span class="op">(</span><span class="st">"S. pyogenes"</span><span class="op">)</span> <span class="co"># will remain species: B_STRPT_PYGN</span>
|
||||
<span class="fu">as.mo</span><span class="op">(</span><span class="st">"S. pyogenes"</span>, Lancefield <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span> <span class="co"># will not remain species: B_STRPT_GRPA</span>
|
||||
|
||||
<span class="co"># All mo_* functions use as.mo() internally too (see ?mo_property):</span>
|
||||
<span class="fu"><a href="mo_property.html">mo_genus</a></span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span> <span class="co"># returns "Escherichia"</span>
|
||||
<span class="fu"><a href="mo_property.html">mo_gramstain</a></span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span> <span class="co"># returns "Gram negative"</span>
|
||||
<span class="fu"><a href="mo_property.html">mo_is_intrinsic_resistant</a></span><span class="op">(</span><span class="st">"E. coli"</span>, <span class="st">"vanco"</span><span class="op">)</span> <span class="co"># returns TRUE</span>
|
||||
<span class="co"># }</span>
|
||||
</code></pre></div>
|
||||
<div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># \donttest{</span></span>
|
||||
<span><span class="co"># These examples all return "B_STPHY_AURS", the ID of S. aureus:</span></span>
|
||||
<span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"sau"</span><span class="op">)</span> <span class="co"># WHONET code</span></span>
|
||||
<span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"stau"</span><span class="op">)</span></span>
|
||||
<span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"STAU"</span><span class="op">)</span></span>
|
||||
<span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"staaur"</span><span class="op">)</span></span>
|
||||
<span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"S. aureus"</span><span class="op">)</span></span>
|
||||
<span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"S aureus"</span><span class="op">)</span></span>
|
||||
<span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"Staphylococcus aureus"</span><span class="op">)</span></span>
|
||||
<span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"Staphylococcus aureus (MRSA)"</span><span class="op">)</span></span>
|
||||
<span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"Zthafilokkoockus oureuz"</span><span class="op">)</span> <span class="co"># handles incorrect spelling</span></span>
|
||||
<span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"MRSA"</span><span class="op">)</span> <span class="co"># Methicillin Resistant S. aureus</span></span>
|
||||
<span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"VISA"</span><span class="op">)</span> <span class="co"># Vancomycin Intermediate S. aureus</span></span>
|
||||
<span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"VRSA"</span><span class="op">)</span> <span class="co"># Vancomycin Resistant S. aureus</span></span>
|
||||
<span><span class="fu">as.mo</span><span class="op">(</span><span class="fl">115329001</span><span class="op">)</span> <span class="co"># SNOMED CT code</span></span>
|
||||
<span></span>
|
||||
<span><span class="co"># Dyslexia is no problem - these all work:</span></span>
|
||||
<span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"Ureaplasma urealyticum"</span><span class="op">)</span></span>
|
||||
<span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"Ureaplasma urealyticus"</span><span class="op">)</span></span>
|
||||
<span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"Ureaplasmium urealytica"</span><span class="op">)</span></span>
|
||||
<span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"Ureaplazma urealitycium"</span><span class="op">)</span></span>
|
||||
<span></span>
|
||||
<span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"Streptococcus group A"</span><span class="op">)</span></span>
|
||||
<span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"GAS"</span><span class="op">)</span> <span class="co"># Group A Streptococci</span></span>
|
||||
<span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"GBS"</span><span class="op">)</span> <span class="co"># Group B Streptococci</span></span>
|
||||
<span></span>
|
||||
<span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"S. epidermidis"</span><span class="op">)</span> <span class="co"># will remain species: B_STPHY_EPDR</span></span>
|
||||
<span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"S. epidermidis"</span>, Becker <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span> <span class="co"># will not remain species: B_STPHY_CONS</span></span>
|
||||
<span></span>
|
||||
<span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"S. pyogenes"</span><span class="op">)</span> <span class="co"># will remain species: B_STRPT_PYGN</span></span>
|
||||
<span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"S. pyogenes"</span>, Lancefield <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span> <span class="co"># will not remain species: B_STRPT_GRPA</span></span>
|
||||
<span></span>
|
||||
<span><span class="co"># All mo_* functions use as.mo() internally too (see ?mo_property):</span></span>
|
||||
<span><span class="fu"><a href="mo_property.html">mo_genus</a></span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span> <span class="co"># returns "Escherichia"</span></span>
|
||||
<span><span class="fu"><a href="mo_property.html">mo_gramstain</a></span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span> <span class="co"># returns "Gram negative"</span></span>
|
||||
<span><span class="fu"><a href="mo_property.html">mo_is_intrinsic_resistant</a></span><span class="op">(</span><span class="st">"E. coli"</span>, <span class="st">"vanco"</span><span class="op">)</span> <span class="co"># returns TRUE</span></span>
|
||||
<span><span class="co"># }</span></span></code></pre></div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
|
||||
@ -369,7 +402,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p>
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
|
||||
</div>
|
||||
|
||||
</footer></div>
|
||||
|
||||
Reference in New Issue
Block a user