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(v1.6.0.9018) unit tests

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dr. M.S. (Matthijs) Berends 2021-05-04 15:20:43 +02:00
parent 5679ccdaf9
commit 0aca719929
14 changed files with 37 additions and 19 deletions
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2
DESCRIPTION
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@ -1,5 +1,5 @@
Package: AMR
Version: 1.6.0.9017
Version: 1.6.0.9018
Date: 2021-05-04
Title: Antimicrobial Resistance Data Analysis
Authors@R: c(

2
NEWS.md
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@ -1,4 +1,4 @@
# `AMR` 1.6.0.9017
# `AMR` 1.6.0.9018
## <small>Last updated: 4 May 2021</small>
### New

8
R/aa_helper_functions.R
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@ -841,6 +841,14 @@ message_not_thrown_before <- function(fn, entire_session = FALSE) {
is.null(pkg_env[[paste0("thrown_msg.", fn)]]) || !identical(pkg_env[[paste0("thrown_msg.", fn)]], unique_call_id(entire_session))
}
reset_all_thrown_messages <- function() {
# for unit tests, where the environment and highest system call do not change
# can be found in tests/testthat/*.R
pkg_env_contents <- ls(envir = pkg_env)
rm(list = pkg_env_contents[pkg_env_contents %like% "^thrown_msg."],
envir = pkg_env)
}
has_colour <- function() {
# this is a base R version of crayon::has_color, but disables colours on emacs

20
R/rsi.R
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@ -259,12 +259,22 @@ as.rsi.default <- function(x, ...) {
}
if (inherits(x, c("integer", "numeric", "double")) && all(x %in% c(1:3, NA))) {
x <- as.character(x) # this is needed to prevent the vctrs pkg to throw an error
x[x == "1"] <- "S"
x[x == "2"] <- "I"
x[x == "3"] <- "R"
x.bak <- x
x <- as.character(x) # this is needed to prevent the vctrs pkg from throwing an error
} else if (!all(is.na(x)) && !identical(levels(x), c("S", "I", "R")) && !all(x %in% c("R", "S", "I", NA))) {
# support haven package for importing e.g., from SPSS - it adds the 'labels' attribute
lbls <- attributes(x)$labels
if (!is.null(lbls) && all(c("R", "S", "I") %in% names(lbls)) && all(c(1:3) %in% lbls)) {
x[x.bak == 1] <- names(lbls[lbls == 1])
x[x.bak == 2] <- names(lbls[lbls == 2])
x[x.bak == 3] <- names(lbls[lbls == 3])
} else {
x[x.bak == 1] <- "S"
x[x.bak == 2] <- "I"
x[x.bak == 3] <- "R"
}
} else if (!all(is.na(x)) && !identical(levels(x), c("R", "S", "I")) && !all(x %in% c("R", "S", "I", NA))) {
if (all(x %unlike% "(R|S|I)", na.rm = TRUE)) {
# check if they are actually MICs or disks

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data-raw/AMR_latest.tar.gz
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docs/404.html
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@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<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">1.6.0.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9018</span>
</span>
</div>

2
docs/LICENSE-text.html
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@ -81,7 +81,7 @@
</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">1.6.0.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9018</span>
</span>
</div>

2
docs/articles/index.html
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@ -81,7 +81,7 @@
</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">1.6.0.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9018</span>
</span>
</div>

2
docs/authors.html
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@ -81,7 +81,7 @@
</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">1.6.0.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9018</span>
</span>
</div>

2
docs/index.html
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@ -42,7 +42,7 @@
</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">1.6.0.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9018</span>
</span>
</div>

8
docs/news/index.html
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@ -81,7 +81,7 @@
</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">1.6.0.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9018</span>
</span>
</div>
@ -236,9 +236,9 @@
<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
</div>
<div id="amr-1609017" class="section level1">
<h1 class="page-header" data-toc-text="1.6.0.9017">
<a href="#amr-1609017" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.6.0.9017</h1>
<div id="amr-1609018" class="section level1">
<h1 class="page-header" data-toc-text="1.6.0.9018">
<a href="#amr-1609018" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.6.0.9018</h1>
<div id="last-updated-4-may-2021" class="section level2">
<h2 class="hasAnchor">
<a href="#last-updated-4-may-2021" class="anchor"></a><small>Last updated: 4 May 2021</small>

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docs/pkgdown.yml
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@ -12,7 +12,7 @@ articles:
datasets: datasets.html
resistance_predict: resistance_predict.html
welcome_to_AMR: welcome_to_AMR.html
last_built: 2021-05-04T10:36Z
last_built: 2021-05-04T13:19Z
urls:
reference: https://msberends.github.io/AMR//reference
article: https://msberends.github.io/AMR//articles

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docs/reference/index.html
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@ -81,7 +81,7 @@
</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">1.6.0.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9018</span>
</span>
</div>

2
docs/survey.html
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@ -81,7 +81,7 @@
</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">1.6.0.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9018</span>
</span>
</div>