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(v1.2.0.9023) ab_from_text() improvement

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dr. M.S. (Matthijs) Berends
2020-07-02 21:12:52 +02:00
parent 298e67a45b
commit 152ac5bcad
29 changed files with 175 additions and 118 deletions
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2
docs/404.html
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@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="https://msberends.gitlab.io/AMR/index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9022</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9023</span>
</span>
</div>

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docs/LICENSE-text.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">1.2.0.9022</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9023</span>
</span>
</div>

2
docs/articles/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">1.2.0.9022</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9023</span>
</span>
</div>

2
docs/authors.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">1.2.0.9022</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9023</span>
</span>
</div>

2
docs/index.html
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@ -43,7 +43,7 @@
</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">1.2.0.9022</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9023</span>
</span>
</div>

17
docs/news/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">1.2.0.9022</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9023</span>
</span>
</div>
@ -229,13 +229,13 @@
<small>Source: <a href='https://gitlab.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
</div>
<div id="amr-1209022" class="section level1">
<h1 class="page-header" data-toc-text="1.2.0.9022">
<a href="#amr-1209022" class="anchor"></a>AMR 1.2.0.9022<small> Unreleased </small>
<div id="amr-1209023" class="section level1">
<h1 class="page-header" data-toc-text="1.2.0.9023">
<a href="#amr-1209023" class="anchor"></a>AMR 1.2.0.9023<small> Unreleased </small>
</h1>
<div id="last-updated-01-jul-2020" class="section level2">
<div id="last-updated-02-jul-2020" class="section level2">
<h2 class="hasAnchor">
<a href="#last-updated-01-jul-2020" class="anchor"></a><small>Last updated: 01-Jul-2020</small>
<a href="#last-updated-02-jul-2020" class="anchor"></a><small>Last updated: 02-Jul-2020</small>
</h2>
<div id="new" class="section level3">
<h3 class="hasAnchor">
@ -262,10 +262,10 @@
<h3 class="hasAnchor">
<a href="#changed" class="anchor"></a>Changed</h3>
<ul>
<li>Using unexisting columns in all <code>count_*()</code>, <code>proportion_*()</code>, <code><a href="../reference/proportion.html">susceptibility()</a></code> and <code><a href="../reference/proportion.html">resistance()</a></code> functions wil now return an error instead of dropping them silently</li>
<li>Using unexisting columns in all <code>count_*()</code>, <code>proportion_*()</code>, <code><a href="../reference/proportion.html">susceptibility()</a></code> and <code><a href="../reference/proportion.html">resistance()</a></code> functions wil now return an error instead of dropping them silently. Using variables for column names (as well as <code><a href="https://dplyr.tidyverse.org/reference/reexports.html">dplyr::all_of()</a></code>) now works again.</li>
<li>Improvements for <code><a href="../reference/as.ab.html">as.ab()</a></code>:
<ul>
<li>Dramatic improvement of the algorithm behind <code><a href="../reference/as.ab.html">as.ab()</a></code>, making many more input errors translatable like from digitalised health care records, using too few or too many vowels or consonants and many more</li>
<li>Dramatic improvement of the algorithm behind <code><a href="../reference/as.ab.html">as.ab()</a></code>, making many more input errors translatable, such as digitalised health care records, using too few or too many vowels or consonants and many more</li>
<li>Added progress bar</li>
<li>Fixed a bug where <code><a href="../reference/as.ab.html">as.ab()</a></code> would return an error on invalid input values</li>
<li>The <code><a href="../reference/as.ab.html">as.ab()</a></code> function will now throw a note if more than 1 antimicrobial drug could be retrieved from a single input value.</li>
@ -279,6 +279,7 @@
<li>Fixed a bug in <code><a href="../reference/bug_drug_combinations.html">bug_drug_combinations()</a></code> for when only one antibiotic was in the input data</li>
<li>Changed the summary for class <code>&lt;mo&gt;</code>, to highlight the %SI vs. %R</li>
<li>Improved error handling, giving more useful info when functions return an error</li>
<li>Any progress bar will now only show in interactive mode (i.e. not in R Markdown)</li>
</ul>
</div>
</div>

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docs/pkgdown.yml
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@ -10,7 +10,7 @@ articles:
WHONET: WHONET.html
benchmarks: benchmarks.html
resistance_predict: resistance_predict.html
last_built: 2020-07-01T14:20Z
last_built: 2020-07-02T19:12Z
urls:
reference: https://msberends.gitlab.io/AMR/reference
article: https://msberends.gitlab.io/AMR/articles

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docs/reference/AMR.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">1.2.0.9019</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9023</span>
</span>
</div>

7
docs/reference/ab_from_text.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">1.2.0.9019</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9023</span>
</span>
</div>
@ -240,6 +240,7 @@
<span class='kw'>type</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"drug"</span>, <span class='st'>"dose"</span>, <span class='st'>"administration"</span>),
<span class='kw'>collapse</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
<span class='kw'>translate_ab</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
<span class='kw'>thorough_search</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
<span class='no'>...</span>
)</pre>
@ -262,6 +263,10 @@
<th>translate_ab</th>
<td><p>if <code>type = "drug"</code>: a column name of the <a href='antibiotics.html'>antibiotics</a> data set to translate the antibiotic abbreviations to, using <code><a href='ab_property.html'>ab_property()</a></code>. Defaults to <code>FALSE</code>. Using <code>TRUE</code> is equal to using "name".</p></td>
</tr>
<tr>
<th>thorough_search</th>
<td><p>logical to indicate whether the input must be extensively searched for misspelling and other faulty input values. Setting this to <code>TRUE</code> will take considerably more time than when using <code>FALSE</code>. At default, it will turn <code>TRUE</code> when all input elements contain a maximum of three words.</p></td>
</tr>
<tr>
<th>...</th>
<td><p>parameters passed on to <code><a href='as.ab.html'>as.ab()</a></code></p></td>

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docs/reference/as.ab.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">1.2.0.9022</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9023</span>
</span>
</div>

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docs/reference/eucast_rules.html
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@ -83,7 +83,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
</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">1.2.0.9019</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9023</span>
</span>
</div>

2
docs/reference/ggplot_pca.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">1.2.0.9019</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9023</span>
</span>
</div>

2
docs/reference/ggplot_rsi.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">1.2.0.9019</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9023</span>
</span>
</div>

2
docs/reference/guess_ab_col.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">1.2.0.9019</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9023</span>
</span>
</div>

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">1.2.0.9022</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9023</span>
</span>
</div>

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docs/reference/lifecycle.html
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@ -84,7 +84,7 @@ This page contains a section for every lifecycle (with text borrowed from the af
</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">1.2.0.9019</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9023</span>
</span>
</div>

2
docs/reference/mdro.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">1.2.0.9019</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9023</span>
</span>
</div>

2
docs/reference/pca.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">1.2.0.9019</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9023</span>
</span>
</div>

2
docs/reference/resistance_predict.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">1.2.0.9019</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9023</span>
</span>
</div>