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(v0.7.1.9082) CI fix

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dr. M.S. (Matthijs) Berends 2019-09-23 14:37:24 +02:00
parent 64d9829030
commit a8c6b8f9c4
11 changed files with 16 additions and 15 deletions
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2
DESCRIPTION
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@ -1,5 +1,5 @@
Package: AMR Package: AMR
Version: 0.7.1.9081 Version: 0.7.1.9082
Date: 2019-09-23 Date: 2019-09-23
Title: Antimicrobial Resistance Analysis Title: Antimicrobial Resistance Analysis
Authors@R: c( Authors@R: c(

2
NEWS.md
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@ -1,4 +1,4 @@
# AMR 0.7.1.9081 # AMR 0.7.1.9082
<small>Last updated: 23-Sep-2019</small> <small>Last updated: 23-Sep-2019</small>
### Breaking ### Breaking

3
R/bug_drug_combinations.R
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@ -97,7 +97,8 @@ format.bug_drug_combinations <- function(x,
combine_IR = FALSE, combine_IR = FALSE,
add_ab_group = TRUE, add_ab_group = TRUE,
decimal.mark = getOption("OutDec"), decimal.mark = getOption("OutDec"),
big.mark = ifelse(decimal.mark == ",", ".", ",")) { big.mark = ifelse(decimal.mark == ",", ".", ","),
...) {
if (combine_IR == FALSE) { if (combine_IR == FALSE) {
x$isolates <- x$R x$isolates <- x$R
} else { } else {

2
docs/LICENSE-text.html
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@ -78,7 +78,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <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">0.7.1.9081</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9082</span>
</span> </span>
</div> </div>

2
docs/articles/index.html
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@ -78,7 +78,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <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">0.7.1.9081</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9082</span>
</span> </span>
</div> </div>

2
docs/authors.html
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@ -78,7 +78,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <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">0.7.1.9081</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9082</span>
</span> </span>
</div> </div>

2
docs/index.html
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@ -42,7 +42,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <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">0.7.1.9081</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9082</span>
</span> </span>
</div> </div>

8
docs/news/index.html
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@ -78,7 +78,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <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">0.7.1.9081</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9082</span>
</span> </span>
</div> </div>
@ -225,9 +225,9 @@
</div> </div>
<div id="amr-0-7-1-9081" class="section level1"> <div id="amr-0-7-1-9082" class="section level1">
<h1 class="page-header"> <h1 class="page-header">
<a href="#amr-0-7-1-9081" class="anchor"></a>AMR 0.7.1.9081<small> Unreleased </small> <a href="#amr-0-7-1-9082" class="anchor"></a>AMR 0.7.1.9082<small> Unreleased </small>
</h1> </h1>
<p><small>Last updated: 23-Sep-2019</small></p> <p><small>Last updated: 23-Sep-2019</small></p>
<div id="breaking" class="section level3"> <div id="breaking" class="section level3">
@ -1280,7 +1280,7 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
<div id="tocnav"> <div id="tocnav">
<h2>Contents</h2> <h2>Contents</h2>
<ul class="nav nav-pills nav-stacked"> <ul class="nav nav-pills nav-stacked">
<li><a href="#amr-0-7-1-9081">0.7.1.9081</a></li> <li><a href="#amr-0-7-1-9082">0.7.1.9082</a></li>
<li><a href="#amr-0-7-1">0.7.1</a></li> <li><a href="#amr-0-7-1">0.7.1</a></li>
<li><a href="#amr-0-7-0">0.7.0</a></li> <li><a href="#amr-0-7-0">0.7.0</a></li>
<li><a href="#amr-0-6-1">0.6.1</a></li> <li><a href="#amr-0-6-1">0.6.1</a></li>

4
docs/reference/bug_drug_combinations.html
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@ -80,7 +80,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <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">0.7.1.9081</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9082</span>
</span> </span>
</div> </div>
@ -240,7 +240,7 @@
<span class='co'># S3 method for bug_drug_combinations</span> <span class='co'># S3 method for bug_drug_combinations</span>
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/format'>format</a></span>(<span class='no'>x</span>, <span class='kw'>combine_IR</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/format'>format</a></span>(<span class='no'>x</span>, <span class='kw'>combine_IR</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
<span class='kw'>add_ab_group</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>decimal.mark</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/options'>getOption</a></span>(<span class='st'>"OutDec"</span>), <span class='kw'>add_ab_group</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>decimal.mark</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/options'>getOption</a></span>(<span class='st'>"OutDec"</span>),
<span class='kw'>big.mark</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/ifelse'>ifelse</a></span>(<span class='no'>decimal.mark</span> <span class='kw'>==</span> <span class='st'>","</span>, <span class='st'>"."</span>, <span class='st'>","</span>))</pre> <span class='kw'>big.mark</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/ifelse'>ifelse</a></span>(<span class='no'>decimal.mark</span> <span class='kw'>==</span> <span class='st'>","</span>, <span class='st'>"."</span>, <span class='st'>","</span>), <span class='no'>...</span>)</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments"> <table class="ref-arguments">

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docs/reference/index.html
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@ -78,7 +78,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <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">0.7.1.9081</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9082</span>
</span> </span>
</div> </div>

2
man/bug_drug_combinations.Rd
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@ -13,7 +13,7 @@ bug_drug_combinations(x, col_mo = NULL, minimum = 30,
\method{format}{bug_drug_combinations}(x, combine_IR = FALSE, \method{format}{bug_drug_combinations}(x, combine_IR = FALSE,
add_ab_group = TRUE, decimal.mark = getOption("OutDec"), add_ab_group = TRUE, decimal.mark = getOption("OutDec"),
big.mark = ifelse(decimal.mark == ",", ".", ",")) big.mark = ifelse(decimal.mark == ",", ".", ","), ...)
} }
\arguments{ \arguments{
\item{x}{data with antibiotic columns, like e.g. \code{AMX} and \code{AMC}} \item{x}{data with antibiotic columns, like e.g. \code{AMX} and \code{AMC}}