diff --git a/DESCRIPTION b/DESCRIPTION index b62ab3c70..adbff7fb4 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: AMR -Version: 1.3.0.9024 +Version: 1.3.0.9025 Date: 2020-09-19 Title: Antimicrobial Resistance Analysis Authors@R: c( diff --git a/NEWS.md b/NEWS.md index 601bdac27..1dfcf7a2d 100755 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# AMR 1.3.0.9024 +# AMR 1.3.0.9025 ## Last updated: 19 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/docs/404.html b/docs/404.html index f4cc0b851..f74f9078e 100644 --- a/docs/404.html +++ b/docs/404.html @@ -81,7 +81,7 @@ AMR (for R) - 1.3.0.9024 + 1.3.0.9025 diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index b13142644..a8c8cfa82 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -81,7 +81,7 @@ AMR (for R) - 1.3.0.9024 + 1.3.0.9025 diff --git a/docs/articles/index.html b/docs/articles/index.html index 9b2bb8d38..1ecb9f7ea 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.3.0.9024 + 1.3.0.9025 diff --git a/docs/authors.html b/docs/authors.html index 5716e1ca1..746ddb0cd 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -81,7 +81,7 @@ AMR (for R) - 1.3.0.9024 + 1.3.0.9025 diff --git a/docs/index.html b/docs/index.html index c79a78774..9145e540f 100644 --- a/docs/index.html +++ b/docs/index.html @@ -43,7 +43,7 @@ AMR (for R) - 1.3.0.9024 + 1.3.0.9025 diff --git a/docs/news/index.html b/docs/news/index.html index f887c09e9..c2e2df97a 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.3.0.9024 + 1.3.0.9025 @@ -236,9 +236,9 @@ Source: NEWS.md -
-

-AMR 1.3.0.9024 Unreleased +
+

+AMR 1.3.0.9025 Unreleased

diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index c2bcfec32..10e117b75 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: 2020-09-19T10:17Z +last_built: 2020-09-19T13:07Z 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 8f2273b6f..b3c256b67 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.3.0.9024 + 1.3.0.9025

diff --git a/docs/survey.html b/docs/survey.html index 8b1de042a..fac56fb7d 100644 --- a/docs/survey.html +++ b/docs/survey.html @@ -81,7 +81,7 @@ AMR (for R) - 1.3.0.9024 + 1.3.0.9025
diff --git a/tests/testthat/test-eucast_rules.R b/tests/testthat/test-eucast_rules.R index 4943a9f90..59c765763 100755 --- a/tests/testthat/test-eucast_rules.R +++ b/tests/testthat/test-eucast_rules.R @@ -30,7 +30,8 @@ test_that("EUCAST rules work", { c("if_mo_property", "like.is.one_of", "this_value", "and_these_antibiotics", "have_these_values", "then_change_these_antibiotics", "to_value", - "reference.rule", "reference.rule_group")) + "reference.rule", "reference.rule_group", + "reference.version")) expect_error(suppressWarnings(eucast_rules(example_isolates, col_mo = "Non-existing"))) expect_error(eucast_rules(x = "text")) diff --git a/tests/testthat/test-mic.R b/tests/testthat/test-mic.R index f9b689056..437644711 100755 --- a/tests/testthat/test-mic.R +++ b/tests/testthat/test-mic.R @@ -38,10 +38,10 @@ test_that("mic works", { expect_warning(as.mic("INVALID VALUE")) - # print plots - expect_success(x <- barplot(as.mic(c(1, 2, 4, 8)))) - expect_success(x <- plot(as.mic(c(1, 2, 4, 8)))) - expect_success(x <- print(as.mic(c(1, 2, 4, 8)))) + pdf(NULL) # prevent Rplots.pdf being created + expect_silent(barplot(as.mic(c(1, 2, 4, 8)))) + expect_silent(plot(as.mic(c(1, 2, 4, 8)))) + expect_output(print(as.mic(c(1, 2, 4, 8)))) expect_equal(summary(as.mic(c(2, 8))), structure(c("Class" = "mic", diff --git a/tests/testthat/test-resistance_predict.R b/tests/testthat/test-resistance_predict.R index 01ed43de1..3aafb98ba 100644 --- a/tests/testthat/test-resistance_predict.R +++ b/tests/testthat/test-resistance_predict.R @@ -35,8 +35,9 @@ test_that("prediction of rsi works", { expect_true(AMX_R[3] < AMX_R[20]) x <- resistance_predict(example_isolates, col_ab = "AMX", year_min = 2010, model = "binomial") - expect_success(y <- plot(x)) - expect_success(y <- ggplot_rsi_predict(x)) + pdf(NULL) # prevent Rplots.pdf being created + expect_silent(plot(x)) + expect_silent(ggplot_rsi_predict(x)) expect_error(ggplot_rsi_predict(example_isolates)) library(dplyr) diff --git a/tests/testthat/test-rsi.R b/tests/testthat/test-rsi.R index 5a3169669..b13d41bfa 100644 --- a/tests/testthat/test-rsi.R +++ b/tests/testthat/test-rsi.R @@ -28,10 +28,10 @@ test_that("rsi works", { expect_true(as.rsi("I") < as.rsi("R")) expect_true(is.rsi(as.rsi("S"))) - # print plots, should not raise errors - expect_success(x <- barplot(as.rsi(c("S", "I", "R")))) - expect_success(x <- plot(as.rsi(c("S", "I", "R")))) - expect_success(x <- print(as.rsi(c("S", "I", "R")))) + pdf(NULL) # prevent Rplots.pdf being created + expect_silent(barplot(as.rsi(c("S", "I", "R")))) + expect_silent(plot(as.rsi(c("S", "I", "R")))) + expect_output(print(as.rsi(c("S", "I", "R")))) expect_equal(as.character(as.rsi(c(1:3))), c("S", "I", "R"))