diff --git a/DESCRIPTION b/DESCRIPTION index 21f615058..994846b9b 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: AMR -Version: 1.3.0.9026 +Version: 1.3.0.9027 Date: 2020-09-24 Title: Antimicrobial Resistance Analysis Authors@R: c( diff --git a/NEWS.md b/NEWS.md index b56d69016..1867b5501 100755 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# AMR 1.3.0.9026 +# AMR 1.3.0.9027 ## Last updated: 24 September 2020 Note: some changes in this version were suggested by anonymous reviewers from the journal we submitted our manuscipt to. We are those reviewers very grateful for going through our code so thoroughly! diff --git a/R/eucast_rules.R b/R/eucast_rules.R index 85c4b94ce..0ee474886 100755 --- a/R/eucast_rules.R +++ b/R/eucast_rules.R @@ -157,7 +157,7 @@ eucast_rules <- function(x, "\n\nThis may overwrite your existing data if you use e.g.:", "\ndata <- eucast_rules(data, verbose = TRUE)\n\nDo you want to continue?") showQuestion <- import_fn("showQuestion", "rstudioapi", error_on_fail = FALSE) - if (!is.null(showQuestion)) { + if (!is.null(showQuestion) & interactive()) { q_continue <- showQuestion("Using verbose = TRUE with eucast_rules()", txt) } else { q_continue <- utils::menu(choices = c("OK", "Cancel"), graphics = FALSE, title = txt) diff --git a/R/globals.R b/R/globals.R index 85d4f247e..dc6313b73 100755 --- a/R/globals.R +++ b/R/globals.R @@ -54,7 +54,10 @@ globalVariables(c(".rowid", "old_name", "pattern", "R", + "reference.rule_group", + "reference.version", "rsi_translation", + "rowid", "rule_group", "rule_name", "se_max", diff --git a/docs/404.html b/docs/404.html index 5669b238c..d4d5565a3 100644 --- a/docs/404.html +++ b/docs/404.html @@ -81,7 +81,7 @@ AMR (for R) - 1.3.0.9026 + 1.3.0.9027 diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index c47af1704..82c39a181 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -81,7 +81,7 @@ AMR (for R) - 1.3.0.9026 + 1.3.0.9027 diff --git a/docs/articles/index.html b/docs/articles/index.html index 9f9ac964c..4dd9b0d27 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.3.0.9026 + 1.3.0.9027 diff --git a/docs/authors.html b/docs/authors.html index d3584ebd3..8b9286c7a 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -81,7 +81,7 @@ AMR (for R) - 1.3.0.9026 + 1.3.0.9027 diff --git a/docs/index.html b/docs/index.html index a44704e1a..fa1d2f18f 100644 --- a/docs/index.html +++ b/docs/index.html @@ -43,7 +43,7 @@ AMR (for R) - 1.3.0.9026 + 1.3.0.9027 diff --git a/docs/news/index.html b/docs/news/index.html index 003ba3b54..56732ef93 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.3.0.9026 + 1.3.0.9027 @@ -236,9 +236,9 @@ Source: NEWS.md -
-

-AMR 1.3.0.9026 Unreleased +
+

+AMR 1.3.0.9027 Unreleased

diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 1a1eb2cd5..2ef83a0aa 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -2,7 +2,7 @@ pandoc: 2.7.3 pkgdown: 1.5.1.9000 pkgdown_sha: eae56f08694abebf93cdfc0dd8e9ede06d8c815f articles: [] -last_built: 2020-09-23T22:29Z +last_built: 2020-09-23T22:50Z urls: reference: https://msberends.github.io/AMR/reference article: https://msberends.github.io/AMR/articles diff --git a/docs/reference/index.html b/docs/reference/index.html index aa17e4cd0..9a06d9f22 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.3.0.9026 + 1.3.0.9027

diff --git a/docs/survey.html b/docs/survey.html index a002ac0c1..e36851d10 100644 --- a/docs/survey.html +++ b/docs/survey.html @@ -81,7 +81,7 @@ AMR (for R) - 1.3.0.9026 + 1.3.0.9027
diff --git a/tests/testthat/test-ab_property.R b/tests/testthat/test-ab_property.R index 1a5857323..1edfeb58c 100644 --- a/tests/testthat/test-ab_property.R +++ b/tests/testthat/test-ab_property.R @@ -43,7 +43,7 @@ test_that("ab_property works", { expect_identical(ab_ddd("AMX", "oral"), 1.5) expect_identical(ab_ddd("AMX", "oral", units = TRUE), "g") - expect_identical(ab_ddd("AMX", "iv"), 1) + expect_identical(ab_ddd("AMX", "iv"), 3) expect_identical(ab_ddd("AMX", "iv", units = TRUE), "g") expect_identical(ab_name(x = c("AMC", "PLB"), language = NULL), c("Amoxicillin/clavulanic acid", "Polymyxin B")) diff --git a/tests/testthat/test-count.R b/tests/testthat/test-count.R index 02ae9173e..159a3059d 100644 --- a/tests/testthat/test-count.R +++ b/tests/testthat/test-count.R @@ -29,7 +29,7 @@ test_that("counts work", { expect_equal(count_all(example_isolates$AMX), n_rsi(example_isolates$AMX)) # AMX resistance in `example_isolates` - expect_equal(count_R(example_isolates$AMX), 683) + expect_equal(count_R(example_isolates$AMX), 804) expect_equal(count_I(example_isolates$AMX), 3) expect_equal(suppressWarnings(count_S(example_isolates$AMX)), 543) expect_equal(count_R(example_isolates$AMX) + count_I(example_isolates$AMX), diff --git a/tests/testthat/test-first_isolate.R b/tests/testthat/test-first_isolate.R index 292ce7e20..2fee0d05c 100755 --- a/tests/testthat/test-first_isolate.R +++ b/tests/testthat/test-first_isolate.R @@ -74,7 +74,7 @@ test_that("first isolates work", { type = "points", info = TRUE), na.rm = TRUE)), - 1400) + 1399) # first non-ICU isolates expect_equal( diff --git a/tests/testthat/test-proportion.R b/tests/testthat/test-proportion.R index dff399cc0..e7a2feb8a 100755 --- a/tests/testthat/test-proportion.R +++ b/tests/testthat/test-proportion.R @@ -29,8 +29,8 @@ test_that("proportions works", { expect_equal(proportion_SI(example_isolates$AMX), susceptibility(example_isolates$AMX)) # AMX resistance in `example_isolates` - expect_equal(proportion_R(example_isolates$AMX), 0.5557364, tolerance = 0.0001) - expect_equal(proportion_I(example_isolates$AMX), 0.002441009, tolerance = 0.0001) + expect_equal(proportion_R(example_isolates$AMX), 0.5955556, tolerance = 0.0001) + expect_equal(proportion_I(example_isolates$AMX), 0.002222222, tolerance = 0.0001) expect_equal(1 - proportion_R(example_isolates$AMX) - proportion_I(example_isolates$AMX), proportion_S(example_isolates$AMX)) expect_equal(proportion_R(example_isolates$AMX) + proportion_I(example_isolates$AMX),