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AMR
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(v1.0.0.9002) fix lintr

This commit is contained in:
dr. M.S. (Matthijs) Berends 2020-02-20 20:31:42 +01:00
parent bdb26f624f
commit 6408911922
14 changed files with 23 additions and 19 deletions
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2
DESCRIPTION
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@ -1,5 +1,5 @@
Package: AMR
Version: 1.0.0.9001
Version: 1.0.0.9002
Date: 2020-02-20
Title: Antimicrobial Resistance Analysis
Authors@R: c(

4
NEWS.md
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@ -1,5 +1,5 @@
# AMR 1.0.0.9001
# AMR 1.0.0.9002
## <small>Last updated: 20-Feb-2020</small>
### Changed
* Added antibiotic abbreviations for a laboratory manufacturer (GLIMS) for cefuroxime, cefotaxime, ceftazidime, cefepime, cefoxitin and trimethoprim/sulfamethoxazole

2
R/rsi.R
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@ -338,7 +338,7 @@ as.rsi.data.frame <- function(x, col_mo = NULL, guideline = "EUCAST", uti = NULL
}
i <- 0
ab_cols <- colnames(x)[sapply(x, function(y) {
ab_cols <- colnames(x)[sapply(x, function(y) {
i <<- i + 1
check <- is.mic(y) | is.disk(y)
ab <- colnames(x)[i]

3
codecov.yml
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@ -20,8 +20,7 @@
# ==================================================================== #
codecov:
notify:
require_ci_to_pass: no # allow fail
require_ci_to_pass: no # allow fail
ci:
- !appveyor # ignore CI builds by AppVeyor

2
docs/404.html
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@ -78,7 +78,7 @@
</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">1.0.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.0.9002</span>
</span>
</div>

2
docs/LICENSE-text.html
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@ -78,7 +78,7 @@
</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">1.0.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.0.9002</span>
</span>
</div>

2
docs/articles/index.html
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@ -78,7 +78,7 @@
</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">1.0.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.0.9002</span>
</span>
</div>

2
docs/authors.html
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@ -78,7 +78,7 @@
</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">1.0.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.0.9002</span>
</span>
</div>

2
docs/extra.css
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@ -191,7 +191,7 @@ thead ~ tbody {
/* only when it has a header */
border-bottom: 2px solid black;
}
th {
thead th {
text-align: inherit;
}
table a:not(.btn), .table a:not(.btn) {

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">1.0.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.0.9002</span>
</span>
</div>

13
docs/news/index.html
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@ -78,7 +78,7 @@
</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">1.0.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.0.9002</span>
</span>
</div>
@ -219,10 +219,14 @@
</div>
<div id="amr-1009001" class="section level1">
<div id="amr-1009002" class="section level1">
<h1 class="page-header">
<a href="#amr-1009001" class="anchor"></a>AMR 1.0.0.9001<small> Unreleased </small>
<a href="#amr-1009002" class="anchor"></a>AMR 1.0.0.9002<small> Unreleased </small>
</h1>
<div id="last-updated-20-feb-2020" class="section level2">
<h2 class="hasAnchor">
<a href="#last-updated-20-feb-2020" class="anchor"></a><small>Last updated: 20-Feb-2020</small>
</h2>
<div id="changed" class="section level3">
<h3 class="hasAnchor">
<a href="#changed" class="anchor"></a>Changed</h3>
@ -240,6 +244,7 @@
<li><p>Added <code>uti</code> (as abbreviation of urinary tract infections) as parameter to <code><a href="../reference/as.rsi.html">as.rsi()</a></code>, so interpretation of MIC values and disk zones can be made dependent on isolates specifically from UTIs</p></li>
</ul>
</div>
</div>
</div>
<div id="amr-100" class="section level1">
<h1 class="page-header">
@ -1468,7 +1473,7 @@
<div id="tocnav">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#amr-1009001">1.0.0.9001</a></li>
<li><a href="#amr-1009002">1.0.0.9002</a></li>
<li><a href="#amr-100">1.0.0</a></li>
<li><a href="#amr-090">0.9.0</a></li>
<li><a href="#amr-080">0.8.0</a></li>

2
docs/reference/as.rsi.html
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@ -79,7 +79,7 @@
</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">1.0.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.0.9002</span>
</span>
</div>

2
docs/reference/index.html
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@ -78,7 +78,7 @@
</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">1.0.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.0.9002</span>
</span>
</div>

2
pkgdown/extra.css
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@ -191,7 +191,7 @@ thead ~ tbody {
/* only when it has a header */
border-bottom: 2px solid black;
}
th {
thead th {
text-align: inherit;
}
table a:not(.btn), .table a:not(.btn) {