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(v0.7.1.9098) mdro() unit test fix

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dr. M.S. (Matthijs) Berends 2019-10-07 15:12:42 +02:00
parent f479dfce60
commit 5dbff3e170
12 changed files with 22 additions and 22 deletions
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2
DESCRIPTION
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@ -1,5 +1,5 @@
Package: AMR
Version: 0.7.1.9097
Version: 0.7.1.9098
Date: 2019-10-07
Title: Antimicrobial Resistance Analysis
Authors@R: c(

2
NEWS.md
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@ -1,4 +1,4 @@
# AMR 0.7.1.9097
# AMR 0.7.1.9098
<small>Last updated: 07-Oct-2019</small>
### Breaking

2
docs/404.html
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@ -84,7 +84,7 @@
</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">0.7.1.9097</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9098</span>
</span>
</div>

2
docs/LICENSE-text.html
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@ -84,7 +84,7 @@
</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">0.7.1.9097</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9098</span>
</span>
</div>

2
docs/articles/index.html
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@ -84,7 +84,7 @@
</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">0.7.1.9097</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9098</span>
</span>
</div>

2
docs/authors.html
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@ -84,7 +84,7 @@
</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">0.7.1.9097</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9098</span>
</span>
</div>

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">0.7.1.9097</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9098</span>
</span>
</div>

8
docs/news/index.html
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@ -84,7 +84,7 @@
</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">0.7.1.9097</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9098</span>
</span>
</div>
@ -231,9 +231,9 @@
</div>
<div id="amr-0-7-1-9097" class="section level1">
<div id="amr-0-7-1-9098" class="section level1">
<h1 class="page-header">
<a href="#amr-0-7-1-9097" class="anchor"></a>AMR 0.7.1.9097<small> Unreleased </small>
<a href="#amr-0-7-1-9098" class="anchor"></a>AMR 0.7.1.9098<small> Unreleased </small>
</h1>
<p><small>Last updated: 07-Oct-2019</small></p>
<div id="breaking" class="section level3">
@ -1289,7 +1289,7 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
<div id="tocnav">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#amr-0-7-1-9097">0.7.1.9097</a></li>
<li><a href="#amr-0-7-1-9098">0.7.1.9098</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-0-6-1">0.6.1</a></li>

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docs/reference/index.html
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@ -84,7 +84,7 @@
</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">0.7.1.9097</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9098</span>
</span>
</div>

9
git_merge.sh
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@ -23,7 +23,16 @@ echo "• pushed changes to master"
git checkout premaster --quiet
echo "• changed branch back to premaster"
git status --short
echo
read -p "Use R-hub to simulate all CRAN checks (y/N)? " choice
case "$choice" in
y|Y|j|J ) ;;
* ) exit 1;;
esac
Rscript -e "rhub::check(devtools::build(), platform = c('debian-clang-devel', 'debian-gcc-devel', 'fedora-clang-devel', 'fedora-gcc-devel', 'windows-x86_64-devel', 'debian-gcc-patched', 'solaris-x86-patched', 'debian-gcc-release', 'windows-x86_64-release', 'macos-elcapitan-release',
'windows-x86_64-oldrel'))"
echo
# and get stashed changes back
# git stash apply --quiet

8
git_premaster.sh
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@ -90,10 +90,4 @@ echo "•••••••••"
echo "• Done •"
echo "••••••••"
echo
read -p "Upload to R-hub builder (y/N)? " choice
case "$choice" in
y|Y|j|J ) ;;
* ) exit 1;;
esac
Rscript -e "rhub::check_for_cran(devtools::build())"
echo

3
tests/testthat/test-mdro.R
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@ -45,9 +45,6 @@ test_that("mdro works", {
expect_equal(brmo(example_isolates, info = FALSE),
mdro(example_isolates, guideline = "BRMO", info = FALSE))
# still working on German guidelines
expect_error(suppressWarnings(mrgn(example_isolates, info = TRUE)))
# test Dutch P. aeruginosa MDRO
expect_equal(
as.character(mdro(data.frame(mo = as.mo("P. aeruginosa"),