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 -
-

- Unreleased AMR 1.7.1.9026

+
+

+ Unreleased AMR 1.7.1.9027

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)