diff --git a/DESCRIPTION b/DESCRIPTION
index 4c714186..b6d62390 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -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)
diff --git a/NEWS.md b/NEWS.md
index bee40141..7bcd9dce 100755
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,4 +1,4 @@
-# `AMR` 1.7.1.9026
+# `AMR` 1.7.1.9027
## Last updated: 19 August 2021
### Breaking changes
diff --git a/data-raw/AMR_latest.tar.gz b/data-raw/AMR_latest.tar.gz
index c73c1fe0..259411d2 100644
Binary files a/data-raw/AMR_latest.tar.gz and b/data-raw/AMR_latest.tar.gz differ
diff --git a/data-raw/_install_deps.R b/data-raw/_install_deps.R
index c7c6b25d..26a1b61b 100644
--- a/data-raw/_install_deps.R
+++ b/data-raw/_install_deps.R
@@ -24,7 +24,7 @@
# ==================================================================== #
# 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) {
}
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))
diff --git a/docs/articles/datasets.html b/docs/articles/datasets.html
index 912a2d23..ad9eb491 100644
--- a/docs/articles/datasets.html
+++ b/docs/articles/datasets.html
@@ -44,7 +44,7 @@
AMR (for R)
- 1.7.1.9026
+ 1.7.1.9027
diff --git a/docs/news/index.html b/docs/news/index.html
index ce0a01e8..dd67d73b 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -92,7 +92,7 @@
AMR (for R)
- 1.7.1.9026
+ 1.7.1.9027
@@ -240,9 +240,9 @@
Source: NEWS.md
-
-
+
+
Last updated: 19 August 2021
diff --git a/inst/tinytest/test-ab_class_selectors.R b/inst/tinytest/test-ab_class_selectors.R
index 8f46342a..2f9aadee 100644
--- a/inst/tinytest/test-ab_class_selectors.R
+++ b/inst/tinytest/test-ab_class_selectors.R
@@ -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)