diff --git a/DESCRIPTION b/DESCRIPTION index b62ab3c7..adbff7fb 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 601bdac2..1dfcf7a2 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 f4cc0b85..f74f9078 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 b1314264..a8c8cfa8 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 9b2bb8d3..1ecb9f7e 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 5716e1ca..746ddb0c 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 c79a7877..9145e540 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 f887c09e..c2e2df97 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 c2bcfec3..10e117b7 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 8f2273b6..b3c256b6 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 8b1de042..fac56fb7 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 4943a9f9..59c76576 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 f9b68905..43764471 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 01ed43de..3aafb98b 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 5a316966..b13d41bf 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"))