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(v0.7.1.9063) septic_patients -> example_isolates

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2019-08-27 16:45:42 +02:00
parent 7a6fce4eb8
commit 93be16484b
92 changed files with 1143 additions and 818 deletions
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16
tests/testthat/test-mo.R
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@ -147,7 +147,7 @@ test_that("as.mo works", {
# select with one column
expect_identical(
septic_patients[1:10,] %>%
example_isolates[1:10,] %>%
left_join_microorganisms() %>%
select(genus) %>%
as.mo() %>%
@ -157,9 +157,9 @@ test_that("as.mo works", {
# select with two columns
expect_identical(
septic_patients[1:10,] %>%
example_isolates[1:10,] %>%
pull(mo),
septic_patients[1:10,] %>%
example_isolates[1:10,] %>%
left_join_microorganisms() %>%
select(genus, species) %>%
as.mo())
@ -168,13 +168,13 @@ test_that("as.mo works", {
expect_warning(as.mo(c("INVALID", "Yeah, unknown")))
# too many columns
expect_error(septic_patients %>% select(1:3) %>% as.mo())
expect_error(example_isolates %>% select(1:3) %>% as.mo())
# print
expect_output(print(as.mo(c("B_ESCHR_COL", NA))))
# test pull
expect_equal(nrow(septic_patients %>% mutate(mo = as.mo(mo))),
expect_equal(nrow(example_isolates %>% mutate(mo = as.mo(mo))),
2000)
# test data.frame
@ -248,7 +248,7 @@ test_that("as.mo works", {
expect_warning(as.mo("Virus"))
# summary
expect_equal(length(summary(septic_patients$mo)), 6)
expect_equal(length(summary(example_isolates$mo)), 6)
# WHONET codes and NA/NaN
expect_equal(as.character(as.mo(c("xxx", "na", "nan"), debug = TRUE)),
@ -260,7 +260,7 @@ test_that("as.mo works", {
rep("UNKNOWN", 3))
expect_null(mo_failures())
expect_true(septic_patients %>% pull(mo) %>% is.mo())
expect_true(example_isolates %>% pull(mo) %>% is.mo())
# expect_equal(get_mo_code("test", "mo"), "test")
# expect_equal(length(get_mo_code("Escherichia", "genus")),
@ -286,7 +286,7 @@ test_that("as.mo works", {
expect_output(print(tibble(mo = as.mo("B_STRPT_PNE"))))
# assigning and subsetting
x <- septic_patients$mo
x <- example_isolates$mo
expect_s3_class(x[1], "mo")
expect_s3_class(x[[1]], "mo")
expect_s3_class(c(x[1], x[9]), "mo")