diff --git a/DESCRIPTION b/DESCRIPTION index 21f61505..994846b9 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 b56d6901..1867b550 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 85c4b94c..0ee47488 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 85d4f247..dc6313b7 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 5669b238..d4d5565a 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 c47af170..82c39a18 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 9f9ac964..4dd9b0d2 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 d3584ebd..8b9286c7 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 a44704e1..fa1d2f18 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 003ba3b5..56732ef9 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 1a1eb2cd..2ef83a0a 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 aa17e4cd..9a06d9f2 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 a002ac0c..e36851d1 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 1a585732..1edfeb58 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 02ae9173..159a3059 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 292ce7e2..2fee0d05 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 dff399cc..e7a2feb8 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),