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(v1.4.0.9006) bugfix

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dr. M.S. (Matthijs) Berends 2020-10-21 14:40:00 +02:00
parent 9109b9dd62
commit 8f868388ce
13 changed files with 19 additions and 19 deletions
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2
DESCRIPTION
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@ -1,5 +1,5 @@
Package: AMR Package: AMR
Version: 1.4.0.9005 Version: 1.4.0.9006
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 1.4.0.9005 # AMR 1.4.0.9006
## <small>Last updated: 21 October 2020</small> ## <small>Last updated: 21 October 2020</small>
### New ### New

2
R/ggplot_rsi.R
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@ -371,7 +371,7 @@ scale_rsi_colours <- function(colours = c(S = "#61a8ff",
IR = "#ff6961", IR = "#ff6961",
R = "#ff6961")) { R = "#ff6961")) {
stop_ifnot_installed("ggplot2") stop_ifnot_installed("ggplot2")
meet_criteria(colours, allow_class = "character") meet_criteria(colours, allow_class = c("character", "logical"))
# previous colour: palette = "RdYlGn" # previous colour: palette = "RdYlGn"
# previous colours: values = c("#b22222", "#ae9c20", "#7cfc00") # previous colours: values = c("#b22222", "#ae9c20", "#7cfc00")

8
R/like.R
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@ -69,7 +69,7 @@
#' } #' }
like <- function(x, pattern, ignore.case = TRUE) { like <- function(x, pattern, ignore.case = TRUE) {
meet_criteria(x, allow_NA = TRUE) meet_criteria(x, allow_NA = TRUE)
meet_criteria(pattern, allow_class = "character") meet_criteria(pattern, allow_NA = FALSE)
meet_criteria(ignore.case, allow_class = "logical", has_length = 1) meet_criteria(ignore.case, allow_class = "logical", has_length = 1)
# set to fixed if no regex found # set to fixed if no regex found
@ -154,15 +154,15 @@ like <- function(x, pattern, ignore.case = TRUE) {
#' @export #' @export
"%like_case%" <- function(x, pattern) { "%like_case%" <- function(x, pattern) {
meet_criteria(x, allow_NA = TRUE) meet_criteria(x, allow_NA = TRUE)
meet_criteria(pattern, allow_class = "character") meet_criteria(pattern, allow_NA = FALSE)
like(x, pattern, ignore.case = FALSE) like(x, pattern, ignore.case = FALSE)
} }
# don't export his one, it's just for convenience in eucast_rules() # don't export his one, it's just for convenience in eucast_rules()
# match all Klebsiella and Raoultella, but not K. aerogenes: fullname %like_perl% "^(Klebsiella(?! aerogenes)|Raoultella)" # match all Klebsiella and Raoultella, but not K. aerogenes: fullname %like_perl% "^(Klebsiella(?! aerogenes)|Raoultella)"
"%like_perl%" <- function(x, pattern) { "%like_perl%" <- function(x, pattern) {
meet_criteria(x) meet_criteria(x, allow_NA = TRUE)
meet_criteria(pattern, allow_class = "character") meet_criteria(pattern, allow_NA = FALSE)
grepl(x = tolower(x), grepl(x = tolower(x),
pattern = tolower(pattern), pattern = tolower(pattern),
perl = TRUE, perl = TRUE,

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">1.4.0.9005</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9006</span>
</span> </span>
</div> </div>

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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">1.4.0.9005</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9006</span>
</span> </span>
</div> </div>

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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">1.4.0.9005</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9006</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">1.4.0.9005</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9006</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">1.4.0.9005</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9006</span>
</span> </span>
</div> </div>

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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">1.4.0.9005</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9006</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-1409005" class="section level1"> <div id="amr-1409006" class="section level1">
<h1 class="page-header" data-toc-text="1.4.0.9005"> <h1 class="page-header" data-toc-text="1.4.0.9006">
<a href="#amr-1409005" class="anchor"></a>AMR 1.4.0.9005<small> Unreleased </small> <a href="#amr-1409006" class="anchor"></a>AMR 1.4.0.9006<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">

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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: 2020-10-21T11:05Z last_built: 2020-10-21T12:39Z
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

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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">1.4.0.9005</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9006</span>
</span> </span>
</div> </div>

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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">1.4.0.9005</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9006</span>
</span> </span>
</div> </div>