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(v1.3.0.9018) language corrections

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dr. M.S. (Matthijs) Berends
2020-09-14 12:21:23 +02:00
parent 0f6760d427
commit 7b6dd676f7
30 changed files with 364 additions and 252 deletions
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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">1.3.0.9016</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9018</span>
</span>
</div>
@ -249,6 +249,7 @@
allow_uncertain = <span class='fl'>TRUE</span>,
reference_df = <span class='fu'><a href='mo_source.html'>get_mo_source</a></span>(),
ignore_pattern = <span class='fu'><a href='https://rdrr.io/r/base/options.html'>getOption</a></span>(<span class='st'>"AMR_ignore_pattern"</span>),
language = <span class='fu'><a href='translate.html'>get_locale</a></span>(),
<span class='kw'>...</span>
)
@ -289,6 +290,10 @@
<th>ignore_pattern</th>
<td><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><a href='https://rdrr.io/r/base/options.html'>options(AMR_ignore_pattern = "(not reported|contaminated flora)")</a></code>.</p></td>
</tr>
<tr>
<th>language</th>
<td><p>language to translate text like "no growth", which defaults to the system language (see <code><a href='translate.html'>get_locale()</a></code>)</p></td>
</tr>
<tr>
<th>...</th>
<td><p>other parameters passed on to functions</p></td>
@ -347,7 +352,7 @@
</ul>
<p>There are three helper functions that can be run after using the <code>as.mo()</code> function:</p><ul>
<li><p>Use <code>mo_uncertainties()</code> to get a <code><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></code> that prints in a pretty format with all taxonomic names that were guessed. The output contains a score that is based on the human pathogenic prevalence and the <a href='https://en.wikipedia.org/wiki/Levenshtein_distance'>Levenshtein distance</a> between the full taxonomic name and the user input.</p></li>
<li><p>Use <code>mo_uncertainties()</code> to get a <code><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></code> that prints in a pretty format with all taxonomic names that were guessed. The output contains a score that is based on the human pathogenic prevalence and the <a href='https://en.wikipedia.org/wiki/Levenshtein_distance'>Levenshtein distance</a> between the user input and the full taxonomic name.</p></li>
<li><p>Use <code>mo_failures()</code> to get a <code><a href='https://rdrr.io/r/base/character.html'>character</a></code> <code><a href='https://rdrr.io/r/base/vector.html'>vector</a></code> with all values that could not be coerced to a valid value.</p></li>
<li><p>Use <code>mo_renamed()</code> to get a <code><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></code> with all values that could be coerced based on old, previously accepted taxonomic names.</p></li>
</ul>