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(v1.3.0.9029) eucast rules fix, unique()

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2020-09-25 14:44:50 +02:00
parent 1d982a82b4
commit 9667c2994f
32 changed files with 234 additions and 160 deletions
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1
tests/testthat/test-ab.R
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@ -67,6 +67,7 @@ test_that("as.ab works", {
expect_s3_class(x[1], "ab")
expect_s3_class(x[[1]], "ab")
expect_s3_class(c(x[1], x[9]), "ab")
expect_s3_class(unique(x[1], x[9]), "ab")
expect_warning(x[1] <- "invalid code")
expect_warning(x[[1]] <- "invalid code")
expect_warning(c(x[1], "test"))

7
tests/testthat/test-disk.R
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@ -29,8 +29,11 @@ test_that("disk works", {
expect_equal(suppressWarnings(as.logical(as.disk("INVALID VALUE"))), NA)
# all levels should be valid disks
expect_silent(as.disk(levels(as.disk(15))))
x <- as.disk(c(20, 40))
expect_s3_class(x[1], "disk")
expect_s3_class(x[[1]], "disk")
expect_s3_class(c(x[1], x[9]), "disk")
expect_s3_class(unique(x[1], x[9]), "disk")
expect_warning(as.disk("INVALID VALUE"))
expect_output(print(as.disk(12)))

2
tests/testthat/test-ggplot_rsi.R
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@ -29,6 +29,8 @@ test_that("ggplot_rsi works", {
library(dplyr)
library(ggplot2)
pdf(NULL) # prevent Rplots.pdf being created
# data should be equal
expect_equal(

2
tests/testthat/test-import_fn.R
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@ -19,6 +19,8 @@
# Visit our website for more info: https://msberends.github.io/AMR. #
# ==================================================================== #
context("import_fn.R")
test_that("imports work", {
skip_on_cran()

7
tests/testthat/test-mic.R
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@ -34,8 +34,11 @@ test_that("mic works", {
expect_equal(suppressWarnings(as.logical(as.mic("INVALID VALUE"))), NA)
# all levels should be valid MICs
expect_silent(as.mic(levels(as.mic(1))))
x <- as.mic(c(2, 4))
expect_s3_class(x[1], "mic")
expect_s3_class(x[[1]], "mic")
expect_s3_class(c(x[1], x[9]), "mic")
expect_s3_class(unique(x[1], x[9]), "mic")
expect_warning(as.mic("INVALID VALUE"))
pdf(NULL) # prevent Rplots.pdf being created

2
tests/testthat/test-pca.R
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@ -44,6 +44,8 @@ test_that("PCA works", {
expect_s3_class(pca_model, "pca")
pdf(NULL) # prevent Rplots.pdf being created
ggplot_pca(pca_model, ellipse = TRUE)
ggplot_pca(pca_model, arrows_textangled = FALSE)
})

7
tests/testthat/test-rsi.R
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@ -28,6 +28,13 @@ test_that("rsi works", {
expect_true(as.rsi("I") < as.rsi("R"))
expect_true(is.rsi(as.rsi("S")))
x <- example_isolates$AMX
expect_s3_class(x[1], "rsi")
expect_s3_class(x[[1]], "rsi")
expect_s3_class(c(x[1], x[9]), "rsi")
expect_s3_class(unique(x[1], x[9]), "rsi")
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"))))