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AMR
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freq fix

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dr. M.S. (Matthijs) Berends 2019-05-17 09:09:18 +02:00
parent 5eda991c47
commit c3ae6b7699
5 changed files with 12 additions and 6 deletions
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2
.gitlab-ci.yml
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@ -69,6 +69,7 @@ R-release:
- '*.Rcheck/*'
expire_in: '1 month'
cache:
when: always
key: "r350"
paths:
- installed_deps/
@ -99,6 +100,7 @@ R-devel:
- '*.Rcheck/*'
expire_in: '1 month'
cache:
when: always
key: "r360"
paths:
- installed_deps/

2
DESCRIPTION
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@ -1,6 +1,6 @@
Package: AMR
Version: 0.6.1.9003
Date: 2019-05-16
Date: 2019-05-17
Title: Antimicrobial Resistance Analysis
Authors@R: c(
person(

10
R/freq.R
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@ -585,10 +585,12 @@ format_header <- function(x, markdown = FALSE, decimal.mark = ".", big.mark = ",
# FORMATTING
# rsi
if (has_length == TRUE & any(x_class == "rsi")) {
ab <- tryCatch(as.ab(attributes(x)$opt$vars), error = function(e) NA)
if (!is.na(ab) & isTRUE(length(ab) > 0)) {
header$drug <- paste0(ab_name(ab[1L]), " (", ab[1L], ", ", ab_atc(ab[1L]), ")")
header$group <- ab_group(ab[1L])
if (!is.null(attributes(x)$opt$vars)) {
ab <- tryCatch(as.ab(attributes(x)$opt$vars), error = function(e) NA)
if (!is.na(ab) & isTRUE(length(ab) > 0)) {
header$drug <- paste0(ab_name(ab[1L]), " (", ab[1L], ", ", ab_atc(ab[1L]), ")")
header$group <- ab_group(ab[1L])
}
}
header$`%SI` <- percent(header$count_SI / (header$count_SI + header$count_R),
force_zero = TRUE, round = digits, decimal.mark = decimal.mark)

2
docs/reference/ab_property.html
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@ -259,6 +259,8 @@
<span class='fu'>ab_ddd</span>(<span class='no'>x</span>, <span class='kw'>administration</span> <span class='kw'>=</span> <span class='st'>"oral"</span>, <span class='kw'>units</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)
<span class='fu'>ab_info</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>)
<span class='fu'>ab_property</span>(<span class='no'>x</span>, <span class='kw'>property</span> <span class='kw'>=</span> <span class='st'>"name"</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>)</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>

2
docs/reference/index.html
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@ -379,7 +379,7 @@
</tr><tr>
<td>
<p><code><a href="ab_property.html">ab_name()</a></code> <code><a href="ab_property.html">ab_atc()</a></code> <code><a href="ab_property.html">ab_cid()</a></code> <code><a href="ab_property.html">ab_synonyms()</a></code> <code><a href="ab_property.html">ab_tradenames()</a></code> <code><a href="ab_property.html">ab_group()</a></code> <code><a href="ab_property.html">ab_atc_group1()</a></code> <code><a href="ab_property.html">ab_atc_group2()</a></code> <code><a href="ab_property.html">ab_ddd()</a></code> <code><a href="ab_property.html">ab_property()</a></code> </p>
<p><code><a href="ab_property.html">ab_name()</a></code> <code><a href="ab_property.html">ab_atc()</a></code> <code><a href="ab_property.html">ab_cid()</a></code> <code><a href="ab_property.html">ab_synonyms()</a></code> <code><a href="ab_property.html">ab_tradenames()</a></code> <code><a href="ab_property.html">ab_group()</a></code> <code><a href="ab_property.html">ab_atc_group1()</a></code> <code><a href="ab_property.html">ab_atc_group2()</a></code> <code><a href="ab_property.html">ab_ddd()</a></code> <code><a href="ab_property.html">ab_info()</a></code> <code><a href="ab_property.html">ab_property()</a></code> </p>
</td>
<td><p>Property of an antibiotic</p></td>
</tr><tr>