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AMR
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(v1.2.0.9015) ab_from_text()

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dr. M.S. (Matthijs) Berends 2020-06-25 19:20:50 +02:00
parent 344bbd57f4
commit 033ca49817
13 changed files with 24 additions and 16 deletions
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2
DESCRIPTION
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@ -1,5 +1,5 @@
Package: AMR
Version: 1.2.0.9014
Version: 1.2.0.9015
Date: 2020-06-25
Title: Antimicrobial Resistance Analysis
Authors@R: c(

1
NAMESPACE
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@ -66,6 +66,7 @@ export(ab_atc_group2)
export(ab_cid)
export(ab_class)
export(ab_ddd)
export(ab_from_text)
export(ab_group)
export(ab_info)
export(ab_loinc)

4
NEWS.md
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# AMR 1.2.0.9014
# AMR 1.2.0.9015
## <small>Last updated: 25-Jun-2020</small>
### New
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* Fixed a bug in `bug_drug_combinations()` for when only one antibiotic was in the input data
* Changed the summary for class `<mo>`, to highlight the %SI vs. %R
* Improved error handling, giving more useful info when functions return an error
* Algorithm improvements to `as.ab()`
* Algorithm improvements to `as.ab()`, many more misspellings are now translatable
* Added Monuril as trade name for fosfomycin
# AMR 1.2.0

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R/ab_from_text.R
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#' `df %>% mutate(abx = ab_from_text(clinical_text, collapse = "|"))`
#'
#' This function is also internally used by [as.ab()], although it then only returns the first hit.
#' @export
#' @examples
#' # mind the bad spelling of amoxicillin in this line,
#' # straight from a true health care record:

1
_pkgdown.yml
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@ -94,6 +94,7 @@ reference:
contents:
- starts_with("as.")
- "`eucast_rules`"
- "`ab_from_text`"
- "`guess_ab_col`"
- "`mo_source`"
- title: "Enhancing your data"

2
docs/404.html
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</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">1.2.0.9014</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9015</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">1.2.0.9014</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9015</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">1.2.0.9014</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9015</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">1.2.0.9014</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9015</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">1.2.0.9014</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9015</span>
</span>
</div>

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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">1.2.0.9014</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9015</span>
</span>
</div>
@ -229,9 +229,9 @@
<small>Source: <a href='https://gitlab.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
</div>
<div id="amr-1209014" class="section level1">
<h1 class="page-header" data-toc-text="1.2.0.9014">
<a href="#amr-1209014" class="anchor"></a>AMR 1.2.0.9014<small> Unreleased </small>
<div id="amr-1209015" class="section level1">
<h1 class="page-header" data-toc-text="1.2.0.9015">
<a href="#amr-1209015" class="anchor"></a>AMR 1.2.0.9015<small> Unreleased </small>
</h1>
<div id="last-updated-25-jun-2020" class="section level2">
<h2 class="hasAnchor">
@ -285,8 +285,7 @@
<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>Algorithm improvements to <code><a href="../reference/as.ab.html">as.ab()</a></code>
</li>
<li>Algorithm improvements to <code><a href="../reference/as.ab.html">as.ab()</a></code>, many more misspellings are now translatable</li>
<li>Added Monuril as trade name for fosfomycin</li>
</ul>
</div>

2
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: 2020-06-25T15:34Z
last_built: 2020-06-25T17:20Z
urls:
reference: https://msberends.gitlab.io/AMR/reference
article: https://msberends.gitlab.io/AMR/articles

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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">1.2.0.9014</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9015</span>
</span>
</div>
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<td><p>Apply EUCAST rules</p></td>
</tr><tr>
<td>
<p><code><a href="ab_from_text.html">ab_from_text()</a></code> </p>
</td>
<td><p>Retrieve antimicrobial drugs from text</p></td>
</tr><tr>
<td>
<p><code><a href="guess_ab_col.html">guess_ab_col()</a></code> </p>
</td>