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fix for printing tibbles, improve guess_bactid

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2018-06-08 12:06:54 +02:00
parent efdf5a3dc5
commit 0a5898b17d
12 changed files with 306 additions and 209 deletions
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16
tests/testthat/test-atc.R
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@ -1,6 +1,5 @@
context("atc.R")
test_that("atc_property works", {
expect_equal(tolower(atc_property("J01CA04", property = "Name")), "amoxicillin")
expect_equivalent(atc_property("J01CA04", "DDD"), 1)
@ -15,21 +14,6 @@ test_that("abname works", {
expect_equal(abname("J01CA04", from = 'atc'), "Amoxicillin")
})
test_that("guess_bactid works", {
expect_identical(guess_bactid(c("E. coli", "H. influenzae")), c("ESCCOL", "HAEINF"))
expect_equal(guess_bactid("Escherichia coli"), "ESCCOL")
expect_equal(guess_bactid("Negative rods"), "GNR")
expect_equal(guess_bactid(c("stau",
"STAU",
"staaur",
"S. aureus",
"S aureus",
"Staphylococcus aureus",
"MRSA",
"VISA")),
rep("STAAUR", 8))
})
test_that("guess_atc works", {
expect_equal(guess_atc(c("J01FA01",
"Erythromycin",

40
tests/testthat/test-guess_bactid.R Normal file
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@ -0,0 +1,40 @@
context("guess_bactid.R")
test_that("guess_bactid works", {
expect_identical(
guess_bactid(c("E. coli", "H. influenzae")),
c("ESCCOL", "HAEINF"))
expect_equal(guess_bactid("Escherichia coli"), "ESCCOL")
expect_equal(guess_bactid("Negative rods"), "GNR")
expect_identical(
guess_bactid(c("stau",
"STAU",
"staaur",
"S. aureus",
"S aureus",
"Staphylococcus aureus",
"MRSA",
"VISA")),
rep("STAAUR", 8))
# select with one column
expect_identical(
septic_patients[1:10,] %>%
left_join_microorganisms() %>%
select(genus) %>%
guess_bactid(),
c("STC", "STC", "NEI", "STA", "STA",
"NEI", "ENT", "ENT", "ESC", "KLE"))
# select with two columns
expect_identical(
septic_patients[1:10,] %>%
pull(bactid),
septic_patients[1:10,] %>%
left_join_microorganisms() %>%
select(genus, species) %>%
guess_bactid())
})