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(v0.7.1.9098) mdro() unit test fix
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Package: AMR
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Package: AMR
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Version: 0.7.1.9097
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Version: 0.7.1.9098
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Date: 2019-10-07
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Date: 2019-10-07
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Title: Antimicrobial Resistance Analysis
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Title: Antimicrobial Resistance Analysis
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Authors@R: c(
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Authors@R: c(
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2
NEWS.md
2
NEWS.md
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# AMR 0.7.1.9097
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# AMR 0.7.1.9098
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<small>Last updated: 07-Oct-2019</small>
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<small>Last updated: 07-Oct-2019</small>
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### Breaking
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### Breaking
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@ -84,7 +84,7 @@
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</button>
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</button>
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<span class="navbar-brand">
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<span class="navbar-brand">
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<a class="navbar-link" href="https://msberends.gitlab.io/AMR/index.html">AMR (for R)</a>
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<a class="navbar-link" href="https://msberends.gitlab.io/AMR/index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9097</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9098</span>
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</span>
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</span>
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</div>
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</div>
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@ -84,7 +84,7 @@
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</button>
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</button>
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<span class="navbar-brand">
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<span class="navbar-brand">
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<a class="navbar-link" href="index.html">AMR (for R)</a>
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<a class="navbar-link" href="index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9097</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9098</span>
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</span>
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</span>
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</div>
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</div>
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@ -84,7 +84,7 @@
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</button>
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</button>
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<span class="navbar-brand">
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9097</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9098</span>
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</span>
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</span>
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</div>
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</div>
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@ -84,7 +84,7 @@
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</button>
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</button>
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<span class="navbar-brand">
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<span class="navbar-brand">
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<a class="navbar-link" href="index.html">AMR (for R)</a>
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<a class="navbar-link" href="index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9097</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9098</span>
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</span>
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</span>
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</div>
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</div>
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@ -43,7 +43,7 @@
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</button>
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</button>
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<span class="navbar-brand">
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<span class="navbar-brand">
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<a class="navbar-link" href="index.html">AMR (for R)</a>
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<a class="navbar-link" href="index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9097</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9098</span>
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</span>
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</span>
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</div>
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</div>
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</button>
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</button>
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<span class="navbar-brand">
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9097</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9098</span>
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</span>
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</span>
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</div>
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</div>
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@ -231,9 +231,9 @@
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</div>
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</div>
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<div id="amr-0-7-1-9097" class="section level1">
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<div id="amr-0-7-1-9098" class="section level1">
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<h1 class="page-header">
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<h1 class="page-header">
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<a href="#amr-0-7-1-9097" class="anchor"></a>AMR 0.7.1.9097<small> Unreleased </small>
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<a href="#amr-0-7-1-9098" class="anchor"></a>AMR 0.7.1.9098<small> Unreleased </small>
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</h1>
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</h1>
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<p><small>Last updated: 07-Oct-2019</small></p>
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<p><small>Last updated: 07-Oct-2019</small></p>
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<div id="breaking" class="section level3">
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<div id="breaking" class="section level3">
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@ -1289,7 +1289,7 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
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<div id="tocnav">
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<div id="tocnav">
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<h2>Contents</h2>
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<h2>Contents</h2>
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<ul class="nav nav-pills nav-stacked">
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<ul class="nav nav-pills nav-stacked">
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<li><a href="#amr-0-7-1-9097">0.7.1.9097</a></li>
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<li><a href="#amr-0-7-1-9098">0.7.1.9098</a></li>
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<li><a href="#amr-0-7-1">0.7.1</a></li>
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<li><a href="#amr-0-7-1">0.7.1</a></li>
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<li><a href="#amr-0-7-0">0.7.0</a></li>
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<li><a href="#amr-0-7-0">0.7.0</a></li>
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<li><a href="#amr-0-6-1">0.6.1</a></li>
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<li><a href="#amr-0-6-1">0.6.1</a></li>
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@ -84,7 +84,7 @@
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</button>
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</button>
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<span class="navbar-brand">
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9097</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9098</span>
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</span>
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</span>
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</div>
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</div>
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@ -23,7 +23,16 @@ echo "• pushed changes to master"
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git checkout premaster --quiet
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git checkout premaster --quiet
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echo "• changed branch back to premaster"
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echo "• changed branch back to premaster"
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git status --short
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git status --short
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echo
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read -p "Use R-hub to simulate all CRAN checks (y/N)? " choice
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case "$choice" in
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y|Y|j|J ) ;;
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* ) exit 1;;
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esac
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Rscript -e "rhub::check(devtools::build(), platform = c('debian-clang-devel', 'debian-gcc-devel', 'fedora-clang-devel', 'fedora-gcc-devel', 'windows-x86_64-devel', 'debian-gcc-patched', 'solaris-x86-patched', 'debian-gcc-release', 'windows-x86_64-release', 'macos-elcapitan-release',
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'windows-x86_64-oldrel'))"
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echo
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# and get stashed changes back
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# and get stashed changes back
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# git stash apply --quiet
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# git stash apply --quiet
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echo "• Done •"
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echo "• Done •"
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echo "••••••••"
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echo "••••••••"
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echo
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echo
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read -p "Upload to R-hub builder (y/N)? " choice
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case "$choice" in
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y|Y|j|J ) ;;
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* ) exit 1;;
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esac
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Rscript -e "rhub::check_for_cran(devtools::build())"
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echo
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expect_equal(brmo(example_isolates, info = FALSE),
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expect_equal(brmo(example_isolates, info = FALSE),
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mdro(example_isolates, guideline = "BRMO", info = FALSE))
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mdro(example_isolates, guideline = "BRMO", info = FALSE))
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# still working on German guidelines
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expect_error(suppressWarnings(mrgn(example_isolates, info = TRUE)))
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# test Dutch P. aeruginosa MDRO
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# test Dutch P. aeruginosa MDRO
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expect_equal(
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expect_equal(
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as.character(mdro(data.frame(mo = as.mo("P. aeruginosa"),
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as.character(mdro(data.frame(mo = as.mo("P. aeruginosa"),
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