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AMR
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(v1.4.0.9005) bugfix

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dr. M.S. (Matthijs) Berends 2020-10-21 13:07:23 +02:00
parent ade9f8bafd
commit 9109b9dd62
14 changed files with 24 additions and 24 deletions
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2
DESCRIPTION
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@ -1,5 +1,5 @@
Package: AMR Package: AMR
Version: 1.4.0.9004 Version: 1.4.0.9005
Date: 2020-10-21 Date: 2020-10-21
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 1.4.0.9004 # AMR 1.4.0.9005
## <small>Last updated: 21 October 2020</small> ## <small>Last updated: 21 October 2020</small>
### New ### New

10
R/ggplot_rsi.R
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@ -162,7 +162,7 @@ ggplot_rsi <- function(data,
R = "#ff6961"), R = "#ff6961"),
datalabels = TRUE, datalabels = TRUE,
datalabels.size = 2.5, datalabels.size = 2.5,
datalabels.colour = "gray15", datalabels.colour = "grey15",
title = NULL, title = NULL,
subtitle = NULL, subtitle = NULL,
caption = NULL, caption = NULL,
@ -184,7 +184,7 @@ ggplot_rsi <- function(data,
meet_criteria(minimum, allow_class = c("numeric", "integer"), has_length = 1) meet_criteria(minimum, allow_class = c("numeric", "integer"), has_length = 1)
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE) meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
meet_criteria(nrow, allow_class = c("numeric", "integer"), has_length = 1, allow_NULL = TRUE) meet_criteria(nrow, allow_class = c("numeric", "integer"), has_length = 1, allow_NULL = TRUE)
meet_criteria(colours, allow_class = "character") meet_criteria(colours, allow_class = c("character", "logical"))
meet_criteria(datalabels, allow_class = "logical", has_length = 1) meet_criteria(datalabels, allow_class = "logical", has_length = 1)
meet_criteria(datalabels.size, allow_class = c("numeric", "integer"), has_length = 1) meet_criteria(datalabels.size, allow_class = c("numeric", "integer"), has_length = 1)
meet_criteria(datalabels.colour, allow_class = "character", has_length = 1) meet_criteria(datalabels.colour, allow_class = "character", has_length = 1)
@ -226,8 +226,8 @@ ggplot_rsi <- function(data,
if (fill == "interpretation") { if (fill == "interpretation") {
# set RSI colours # set RSI colours
if (isFALSE(colours) & missing(datalabels.colour)) { if (isFALSE(colours) & missing(datalabels.colour)) {
# set datalabel colour to middle gray # set datalabel colour to middle grey
datalabels.colour <- "gray50" datalabels.colour <- "grey50"
} }
p <- p + scale_rsi_colours(colours = colours) p <- p + scale_rsi_colours(colours = colours)
} }
@ -410,7 +410,7 @@ labels_rsi_count <- function(position = NULL,
combine_SI = TRUE, combine_SI = TRUE,
combine_IR = FALSE, combine_IR = FALSE,
datalabels.size = 3, datalabels.size = 3,
datalabels.colour = "gray15") { datalabels.colour = "grey15") {
stop_ifnot_installed("ggplot2") stop_ifnot_installed("ggplot2")
meet_criteria(position, allow_class = "character", has_length = 1, is_in = c("fill", "stack", "dodge"), allow_NULL = TRUE) meet_criteria(position, allow_class = "character", has_length = 1, is_in = c("fill", "stack", "dodge"), allow_NULL = TRUE)
meet_criteria(x, allow_class = "character", has_length = 1) meet_criteria(x, allow_class = "character", has_length = 1)

2
docs/404.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="https://msberends.github.io/AMR//index.html">AMR (for R)</a> <a class="navbar-link" href="https://msberends.github.io/AMR//index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9004</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9005</span>
</span> </span>
</div> </div>

2
docs/LICENSE-text.html
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@ -81,7 +81,7 @@
</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">1.4.0.9004</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9005</span>
</span> </span>
</div> </div>

2
docs/articles/index.html
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@ -81,7 +81,7 @@
</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">1.4.0.9004</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9005</span>
</span> </span>
</div> </div>

2
docs/authors.html
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@ -81,7 +81,7 @@
</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">1.4.0.9004</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9005</span>
</span> </span>
</div> </div>

2
docs/index.html
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@ -43,7 +43,7 @@
</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">1.4.0.9004</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9005</span>
</span> </span>
</div> </div>

8
docs/news/index.html
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@ -81,7 +81,7 @@
</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">1.4.0.9004</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9005</span>
</span> </span>
</div> </div>
@ -236,9 +236,9 @@
<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small> <small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
</div> </div>
<div id="amr-1409004" class="section level1"> <div id="amr-1409005" class="section level1">
<h1 class="page-header" data-toc-text="1.4.0.9004"> <h1 class="page-header" data-toc-text="1.4.0.9005">
<a href="#amr-1409004" class="anchor"></a>AMR 1.4.0.9004<small> Unreleased </small> <a href="#amr-1409005" class="anchor"></a>AMR 1.4.0.9005<small> Unreleased </small>
</h1> </h1>
<div id="last-updated-21-october-2020" class="section level2"> <div id="last-updated-21-october-2020" class="section level2">
<h2 class="hasAnchor"> <h2 class="hasAnchor">

2
docs/pkgdown.yml
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@ -12,7 +12,7 @@ articles:
datasets: datasets.html datasets: datasets.html
resistance_predict: resistance_predict.html resistance_predict: resistance_predict.html
welcome_to_AMR: welcome_to_AMR.html welcome_to_AMR: welcome_to_AMR.html
last_built: 2020-10-21T09:40Z last_built: 2020-10-21T11:05Z
urls: urls:
reference: https://msberends.github.io/AMR//reference reference: https://msberends.github.io/AMR//reference
article: https://msberends.github.io/AMR//articles article: https://msberends.github.io/AMR//articles

6
docs/reference/ggplot_rsi.html
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@ -82,7 +82,7 @@
</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">1.4.0.9000</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9005</span>
</span> </span>
</div> </div>
@ -260,7 +260,7 @@
<span class='st'>"#ff6961"</span><span class='op'>)</span>, <span class='st'>"#ff6961"</span><span class='op'>)</span>,
datalabels <span class='op'>=</span> <span class='cn'>TRUE</span>, datalabels <span class='op'>=</span> <span class='cn'>TRUE</span>,
datalabels.size <span class='op'>=</span> <span class='fl'>2.5</span>, datalabels.size <span class='op'>=</span> <span class='fl'>2.5</span>,
datalabels.colour <span class='op'>=</span> <span class='st'>"gray15"</span>, datalabels.colour <span class='op'>=</span> <span class='st'>"grey15"</span>,
title <span class='op'>=</span> <span class='cn'>NULL</span>, title <span class='op'>=</span> <span class='cn'>NULL</span>,
subtitle <span class='op'>=</span> <span class='cn'>NULL</span>, subtitle <span class='op'>=</span> <span class='cn'>NULL</span>,
caption <span class='op'>=</span> <span class='cn'>NULL</span>, caption <span class='op'>=</span> <span class='cn'>NULL</span>,
@ -301,7 +301,7 @@
combine_SI <span class='op'>=</span> <span class='cn'>TRUE</span>, combine_SI <span class='op'>=</span> <span class='cn'>TRUE</span>,
combine_IR <span class='op'>=</span> <span class='cn'>FALSE</span>, combine_IR <span class='op'>=</span> <span class='cn'>FALSE</span>,
datalabels.size <span class='op'>=</span> <span class='fl'>3</span>, datalabels.size <span class='op'>=</span> <span class='fl'>3</span>,
datalabels.colour <span class='op'>=</span> <span class='st'>"gray15"</span> datalabels.colour <span class='op'>=</span> <span class='st'>"grey15"</span>
<span class='op'>)</span></pre> <span class='op'>)</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>

2
docs/reference/index.html
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@ -81,7 +81,7 @@
</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">1.4.0.9004</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9005</span>
</span> </span>
</div> </div>

2
docs/survey.html
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@ -81,7 +81,7 @@
</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">1.4.0.9004</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9005</span>
</span> </span>
</div> </div>

4
man/ggplot_rsi.Rd
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@ -28,7 +28,7 @@ ggplot_rsi(
"#ff6961"), "#ff6961"),
datalabels = TRUE, datalabels = TRUE,
datalabels.size = 2.5, datalabels.size = 2.5,
datalabels.colour = "gray15", datalabels.colour = "grey15",
title = NULL, title = NULL,
subtitle = NULL, subtitle = NULL,
caption = NULL, caption = NULL,
@ -69,7 +69,7 @@ labels_rsi_count(
combine_SI = TRUE, combine_SI = TRUE,
combine_IR = FALSE, combine_IR = FALSE,
datalabels.size = 3, datalabels.size = 3,
datalabels.colour = "gray15" datalabels.colour = "grey15"
) )
} }
\arguments{ \arguments{