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(v1.7.1.9027) fix unit test
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Package: AMR
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Package: AMR
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Version: 1.7.1.9026
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Version: 1.7.1.9027
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Date: 2021-08-19
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Date: 2021-08-19
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Title: Antimicrobial Resistance Data Analysis
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Title: Antimicrobial Resistance Data Analysis
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Description: Functions to simplify and standardise antimicrobial resistance (AMR)
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Description: Functions to simplify and standardise antimicrobial resistance (AMR)
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2
NEWS.md
2
NEWS.md
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# `AMR` 1.7.1.9026
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# `AMR` 1.7.1.9027
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## <small>Last updated: 19 August 2021</small>
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## <small>Last updated: 19 August 2021</small>
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### Breaking changes
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### Breaking changes
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# ==================================================================== #
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# ==================================================================== #
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# some old R instances have trouble installing tinytest, so we ship it too
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# some old R instances have trouble installing tinytest, so we ship it too
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install.packages("data-raw/tinytest_1.2.4.10.tar.gz")
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install.packages("data-raw/tinytest_1.2.4.10.tar.gz", dependencies = c("Depends", "Imports"))
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install.packages("data-raw/AMR_latest.tar.gz", dependencies = FALSE)
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install.packages("data-raw/AMR_latest.tar.gz", dependencies = FALSE)
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pkg_suggests <- gsub("[^a-zA-Z0-9]+", "",
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pkg_suggests <- gsub("[^a-zA-Z0-9]+", "",
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@ -39,7 +39,7 @@ if (length(to_install) == 0) {
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}
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}
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for (i in seq_len(length(to_install))) {
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for (i in seq_len(length(to_install))) {
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cat("Installing package", to_install[i], "\n")
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cat("Installing package", to_install[i], "\n")
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tryCatch(install.packages(to_install[i], repos = "https://cran.rstudio.com/", dependencies = TRUE, quiet = FALSE),
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tryCatch(install.packages(to_install[i], repos = "https://cran.rstudio.com/", dependencies = c("Depends", "Imports"), quiet = FALSE),
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# message = function(m) invisible(),
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# message = function(m) invisible(),
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warning = function(w) message(w$message),
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warning = function(w) message(w$message),
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error = function(e) message(e$message))
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error = function(e) message(e$message))
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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">1.7.1.9026</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9027</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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@ -92,7 +92,7 @@
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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">1.7.1.9026</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9027</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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@ -240,9 +240,9 @@
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<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
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<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
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</div>
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</div>
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<div id="amr-1719026" class="section level1">
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<div id="amr-1719027" class="section level1">
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<h1 class="page-header" data-toc-text="1.7.1.9026">
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<h1 class="page-header" data-toc-text="1.7.1.9027">
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<a href="#amr-1719026" class="anchor" aria-hidden="true"></a><small> Unreleased </small><code>AMR</code> 1.7.1.9026</h1>
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<a href="#amr-1719027" class="anchor" aria-hidden="true"></a><small> Unreleased </small><code>AMR</code> 1.7.1.9027</h1>
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<div id="last-updated-19-august-2021" class="section level2">
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<div id="last-updated-19-august-2021" class="section level2">
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<h2 class="hasAnchor">
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<h2 class="hasAnchor">
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<a href="#last-updated-19-august-2021" class="anchor" aria-hidden="true"></a><small>Last updated: 19 August 2021</small>
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<a href="#last-updated-19-august-2021" class="anchor" aria-hidden="true"></a><small>Last updated: 19 August 2021</small>
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@ -24,38 +24,38 @@
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# ==================================================================== #
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# ==================================================================== #
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# antibiotic class selectors
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# antibiotic class selectors
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expect_true(ncol(example_isolates[, ab_class("antimyco"), drop = FALSE]) < ncol(example_isolates))
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expect_equal(ncol(example_isolates[, ab_class("antimyco"), drop = FALSE]), 1, tolerance = 0.5)
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expect_true(ncol(example_isolates[, aminoglycosides(), drop = FALSE]) < ncol(example_isolates))
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expect_equal(ncol(example_isolates[, aminoglycosides(), drop = FALSE]), 4, tolerance = 0.5)
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expect_true(ncol(example_isolates[, aminopenicillins(), drop = FALSE]) < ncol(example_isolates))
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expect_equal(ncol(example_isolates[, aminopenicillins(), drop = FALSE]), 2, tolerance = 0.5)
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expect_true(ncol(example_isolates[, betalactams(), drop = FALSE]) < ncol(example_isolates))
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expect_equal(ncol(example_isolates[, betalactams(), drop = FALSE]), 16, tolerance = 0.5)
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expect_true(ncol(example_isolates[, carbapenems(), drop = FALSE]) < ncol(example_isolates))
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expect_equal(ncol(example_isolates[, carbapenems(), drop = FALSE]), 2, tolerance = 0.5)
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expect_true(ncol(example_isolates[, cephalosporins(), drop = FALSE]) < ncol(example_isolates))
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expect_equal(ncol(example_isolates[, cephalosporins(), drop = FALSE]), 7, tolerance = 0.5)
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expect_true(ncol(example_isolates[, cephalosporins_1st(), drop = FALSE]) < ncol(example_isolates))
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expect_equal(ncol(example_isolates[, cephalosporins_1st(), drop = FALSE]), 1, tolerance = 0.5)
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expect_true(ncol(example_isolates[, cephalosporins_2nd(), drop = FALSE]) < ncol(example_isolates))
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expect_equal(ncol(example_isolates[, cephalosporins_2nd(), drop = FALSE]), 2, tolerance = 0.5)
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expect_true(ncol(example_isolates[, cephalosporins_3rd(), drop = FALSE]) < ncol(example_isolates))
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expect_equal(ncol(example_isolates[, cephalosporins_3rd(), drop = FALSE]), 3, tolerance = 0.5)
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expect_true(ncol(example_isolates[, cephalosporins_4th(), drop = FALSE]) < ncol(example_isolates))
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expect_equal(ncol(example_isolates[, cephalosporins_4th(), drop = FALSE]), 1, tolerance = 0.5)
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expect_true(ncol(example_isolates[, cephalosporins_5th(), drop = FALSE]) < ncol(example_isolates))
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expect_equal(ncol(example_isolates[, cephalosporins_5th(), drop = FALSE]), 0, tolerance = 0.5)
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expect_true(ncol(example_isolates[, fluoroquinolones(), drop = FALSE]) < ncol(example_isolates))
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expect_equal(ncol(example_isolates[, fluoroquinolones(), drop = FALSE]), 2, tolerance = 0.5)
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expect_true(ncol(example_isolates[, glycopeptides(), drop = FALSE]) < ncol(example_isolates))
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expect_equal(ncol(example_isolates[, glycopeptides(), drop = FALSE]), 2, tolerance = 0.5)
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expect_true(ncol(example_isolates[, lincosamides(), drop = FALSE]) < ncol(example_isolates))
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expect_equal(ncol(example_isolates[, lincosamides(), drop = FALSE]), 1, tolerance = 0.5)
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expect_true(ncol(example_isolates[, lipoglycopeptides(), drop = FALSE]) < ncol(example_isolates))
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expect_equal(ncol(example_isolates[, lipoglycopeptides(), drop = FALSE]), 0, tolerance = 0.5)
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expect_true(ncol(example_isolates[, macrolides(), drop = FALSE]) < ncol(example_isolates))
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expect_equal(ncol(example_isolates[, macrolides(), drop = FALSE]), 2, tolerance = 0.5)
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expect_true(ncol(example_isolates[, oxazolidinones(), drop = FALSE]) < ncol(example_isolates))
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expect_equal(ncol(example_isolates[, oxazolidinones(), drop = FALSE]), 1, tolerance = 0.5)
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expect_true(ncol(example_isolates[, penicillins(), drop = FALSE]) < ncol(example_isolates))
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expect_equal(ncol(example_isolates[, penicillins(), drop = FALSE]), 7, tolerance = 0.5)
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expect_true(ncol(example_isolates[, polymyxins(), drop = FALSE]) < ncol(example_isolates))
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expect_equal(ncol(example_isolates[, polymyxins(), drop = FALSE]), 1, tolerance = 0.5)
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expect_true(ncol(example_isolates[, streptogramins(), drop = FALSE]) < ncol(example_isolates))
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expect_equal(ncol(example_isolates[, streptogramins(), drop = FALSE]), 0, tolerance = 0.5)
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expect_true(ncol(example_isolates[, quinolones(), drop = FALSE]) < ncol(example_isolates))
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expect_equal(ncol(example_isolates[, quinolones(), drop = FALSE]), 2, tolerance = 0.5)
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expect_true(ncol(example_isolates[, tetracyclines(), drop = FALSE]) < ncol(example_isolates))
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expect_equal(ncol(example_isolates[, tetracyclines(), drop = FALSE]), 3, tolerance = 0.5)
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expect_true(ncol(example_isolates[, trimethoprims(), drop = FALSE]) < ncol(example_isolates))
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expect_equal(ncol(example_isolates[, trimethoprims(), drop = FALSE]), 2, tolerance = 0.5)
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expect_true(ncol(example_isolates[, ureidopenicillins(), drop = FALSE]) < ncol(example_isolates))
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expect_equal(ncol(example_isolates[, ureidopenicillins(), drop = FALSE]), 1, tolerance = 0.5)
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# Examples:
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# Examples:
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# select columns 'mo', 'AMK', 'GEN', 'KAN' and 'TOB'
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# select columns 'mo', 'AMK', 'GEN', 'KAN' and 'TOB'
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expect_equal(ncol(example_isolates[, c("mo", aminoglycosides())]), 5, tolerance = 0.5)
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expect_equal(ncol(example_isolates[, c("mo", aminoglycosides())]), 5, tolerance = 0.5)
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expect_equal(ncol(example_isolates[, c(administerable_per_os() & penicillins())]), 5, tolerance = 0.5)
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expect_equal(ncol(example_isolates[, c(administrable_per_os() & penicillins())]), 5, tolerance = 0.5)
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expect_equal(ncol(example_isolates[, c(administerable_iv() & penicillins())]), 7, tolerance = 0.5)
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expect_equal(ncol(example_isolates[, c(administrable_iv() & penicillins())]), 7, tolerance = 0.5)
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# filter using any() or all()
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# filter using any() or all()
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expect_equal(nrow(example_isolates[any(carbapenems() == "R"), ]), 55, tolerance = 0.5)
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expect_equal(nrow(example_isolates[any(carbapenems() == "R"), ]), 55, tolerance = 0.5)
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