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(v1.7.1.9027) fix unit test

new-mo-algorithm
parent
commit
41f35c73cd
  1. 2
      DESCRIPTION
  2. 2
      NEWS.md
  3. BIN
      data-raw/AMR_latest.tar.gz
  4. 4
      data-raw/_install_deps.R
  5. 2
      docs/articles/datasets.html
  6. 8
      docs/news/index.html
  7. 52
      inst/tinytest/test-ab_class_selectors.R

2
DESCRIPTION

@ -1,5 +1,5 @@ @@ -1,5 +1,5 @@
Package: AMR
Version: 1.7.1.9026
Version: 1.7.1.9027
Date: 2021-08-19
Title: Antimicrobial Resistance Data Analysis
Description: Functions to simplify and standardise antimicrobial resistance (AMR)

2
NEWS.md

@ -1,4 +1,4 @@ @@ -1,4 +1,4 @@
# `AMR` 1.7.1.9026
# `AMR` 1.7.1.9027
## <small>Last updated: 19 August 2021</small>
### Breaking changes

BIN
data-raw/AMR_latest.tar.gz

Binary file not shown.

4
data-raw/_install_deps.R

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# ==================================================================== #
# some old R instances have trouble installing tinytest, so we ship it too
install.packages("data-raw/tinytest_1.2.4.10.tar.gz")
install.packages("data-raw/tinytest_1.2.4.10.tar.gz", dependencies = c("Depends", "Imports"))
install.packages("data-raw/AMR_latest.tar.gz", dependencies = FALSE)
pkg_suggests <- gsub("[^a-zA-Z0-9]+", "",
@ -39,7 +39,7 @@ if (length(to_install) == 0) { @@ -39,7 +39,7 @@ if (length(to_install) == 0) {
}
for (i in seq_len(length(to_install))) {
cat("Installing package", to_install[i], "\n")
tryCatch(install.packages(to_install[i], repos = "https://cran.rstudio.com/", dependencies = TRUE, quiet = FALSE),
tryCatch(install.packages(to_install[i], repos = "https://cran.rstudio.com/", dependencies = c("Depends", "Imports"), quiet = FALSE),
# message = function(m) invisible(),
warning = function(w) message(w$message),
error = function(e) message(e$message))

2
docs/articles/datasets.html

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</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">1.7.1.9026</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9027</span>
</span>
</div>

8
docs/news/index.html

@ -92,7 +92,7 @@ @@ -92,7 +92,7 @@
</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">1.7.1.9026</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9027</span>
</span>
</div>
@ -240,9 +240,9 @@ @@ -240,9 +240,9 @@
<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
</div>
<div id="amr-1719026" class="section level1">
<h1 class="page-header" data-toc-text="1.7.1.9026">
<a href="#amr-1719026" class="anchor" aria-hidden="true"></a><small> Unreleased </small><code>AMR</code> 1.7.1.9026</h1>
<div id="amr-1719027" class="section level1">
<h1 class="page-header" data-toc-text="1.7.1.9027">
<a href="#amr-1719027" class="anchor" aria-hidden="true"></a><small> Unreleased </small><code>AMR</code> 1.7.1.9027</h1>
<div id="last-updated-19-august-2021" class="section level2">
<h2 class="hasAnchor">
<a href="#last-updated-19-august-2021" class="anchor" aria-hidden="true"></a><small>Last updated: 19 August 2021</small>

52
inst/tinytest/test-ab_class_selectors.R

@ -24,38 +24,38 @@ @@ -24,38 +24,38 @@
# ==================================================================== #
# antibiotic class selectors
expect_true(ncol(example_isolates[, ab_class("antimyco"), drop = FALSE]) < ncol(example_isolates))
expect_true(ncol(example_isolates[, aminoglycosides(), drop = FALSE]) < ncol(example_isolates))
expect_true(ncol(example_isolates[, aminopenicillins(), drop = FALSE]) < ncol(example_isolates))
expect_true(ncol(example_isolates[, betalactams(), drop = FALSE]) < ncol(example_isolates))
expect_true(ncol(example_isolates[, carbapenems(), drop = FALSE]) < ncol(example_isolates))
expect_true(ncol(example_isolates[, cephalosporins(), drop = FALSE]) < ncol(example_isolates))
expect_true(ncol(example_isolates[, cephalosporins_1st(), drop = FALSE]) < ncol(example_isolates))
expect_true(ncol(example_isolates[, cephalosporins_2nd(), drop = FALSE]) < ncol(example_isolates))
expect_true(ncol(example_isolates[, cephalosporins_3rd(), drop = FALSE]) < ncol(example_isolates))
expect_true(ncol(example_isolates[, cephalosporins_4th(), drop = FALSE]) < ncol(example_isolates))
expect_true(ncol(example_isolates[, cephalosporins_5th(), drop = FALSE]) < ncol(example_isolates))
expect_true(ncol(example_isolates[, fluoroquinolones(), drop = FALSE]) < ncol(example_isolates))
expect_true(ncol(example_isolates[, glycopeptides(), drop = FALSE]) < ncol(example_isolates))
expect_true(ncol(example_isolates[, lincosamides(), drop = FALSE]) < ncol(example_isolates))
expect_true(ncol(example_isolates[, lipoglycopeptides(), drop = FALSE]) < ncol(example_isolates))
expect_true(ncol(example_isolates[, macrolides(), drop = FALSE]) < ncol(example_isolates))
expect_true(ncol(example_isolates[, oxazolidinones(), drop = FALSE]) < ncol(example_isolates))
expect_true(ncol(example_isolates[, penicillins(), drop = FALSE]) < ncol(example_isolates))
expect_true(ncol(example_isolates[, polymyxins(), drop = FALSE]) < ncol(example_isolates))
expect_true(ncol(example_isolates[, streptogramins(), drop = FALSE]) < ncol(example_isolates))
expect_true(ncol(example_isolates[, quinolones(), drop = FALSE]) < ncol(example_isolates))
expect_true(ncol(example_isolates[, tetracyclines(), drop = FALSE]) < ncol(example_isolates))
expect_true(ncol(example_isolates[, trimethoprims(), drop = FALSE]) < ncol(example_isolates))
expect_true(ncol(example_isolates[, ureidopenicillins(), drop = FALSE]) < ncol(example_isolates))
expect_equal(ncol(example_isolates[, ab_class("antimyco"), drop = FALSE]), 1, tolerance = 0.5)
expect_equal(ncol(example_isolates[, aminoglycosides(), drop = FALSE]), 4, tolerance = 0.5)
expect_equal(ncol(example_isolates[, aminopenicillins(), drop = FALSE]), 2, tolerance = 0.5)
expect_equal(ncol(example_isolates[, betalactams(), drop = FALSE]), 16, tolerance = 0.5)
expect_equal(ncol(example_isolates[, carbapenems(), drop = FALSE]), 2, tolerance = 0.5)
expect_equal(ncol(example_isolates[, cephalosporins(), drop = FALSE]), 7, tolerance = 0.5)
expect_equal(ncol(example_isolates[, cephalosporins_1st(), drop = FALSE]), 1, tolerance = 0.5)
expect_equal(ncol(example_isolates[, cephalosporins_2nd(), drop = FALSE]), 2, tolerance = 0.5)
expect_equal(ncol(example_isolates[, cephalosporins_3rd(), drop = FALSE]), 3, tolerance = 0.5)
expect_equal(ncol(example_isolates[, cephalosporins_4th(), drop = FALSE]), 1, tolerance = 0.5)
expect_equal(ncol(example_isolates[, cephalosporins_5th(), drop = FALSE]), 0, tolerance = 0.5)
expect_equal(ncol(example_isolates[, fluoroquinolones(), drop = FALSE]), 2, tolerance = 0.5)
expect_equal(ncol(example_isolates[, glycopeptides(), drop = FALSE]), 2, tolerance = 0.5)
expect_equal(ncol(example_isolates[, lincosamides(), drop = FALSE]), 1, tolerance = 0.5)
expect_equal(ncol(example_isolates[, lipoglycopeptides(), drop = FALSE]), 0, tolerance = 0.5)
expect_equal(ncol(example_isolates[, macrolides(), drop = FALSE]), 2, tolerance = 0.5)
expect_equal(ncol(example_isolates[, oxazolidinones(), drop = FALSE]), 1, tolerance = 0.5)
expect_equal(ncol(example_isolates[, penicillins(), drop = FALSE]), 7, tolerance = 0.5)
expect_equal(ncol(example_isolates[, polymyxins(), drop = FALSE]), 1, tolerance = 0.5)
expect_equal(ncol(example_isolates[, streptogramins(), drop = FALSE]), 0, tolerance = 0.5)
expect_equal(ncol(example_isolates[, quinolones(), drop = FALSE]), 2, tolerance = 0.5)
expect_equal(ncol(example_isolates[, tetracyclines(), drop = FALSE]), 3, tolerance = 0.5)
expect_equal(ncol(example_isolates[, trimethoprims(), drop = FALSE]), 2, tolerance = 0.5)
expect_equal(ncol(example_isolates[, ureidopenicillins(), drop = FALSE]), 1, tolerance = 0.5)
# Examples:
# select columns 'mo', 'AMK', 'GEN', 'KAN' and 'TOB'
expect_equal(ncol(example_isolates[, c("mo", aminoglycosides())]), 5, tolerance = 0.5)
expect_equal(ncol(example_isolates[, c(administerable_per_os() & penicillins())]), 5, tolerance = 0.5)
expect_equal(ncol(example_isolates[, c(administerable_iv() & penicillins())]), 7, tolerance = 0.5)
expect_equal(ncol(example_isolates[, c(administrable_per_os() & penicillins())]), 5, tolerance = 0.5)
expect_equal(ncol(example_isolates[, c(administrable_iv() & penicillins())]), 7, tolerance = 0.5)
# filter using any() or all()
expect_equal(nrow(example_isolates[any(carbapenems() == "R"), ]), 55, tolerance = 0.5)

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