AMR/tests/testthat/test-bactid.R

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2018-07-23 14:14:03 +02:00
context("bactid.R")
test_that("as.bactid works", {
expect_identical(
as.character(as.bactid(c("E. coli", "H. influenzae"))),
c("ESCCOL", "HAEINF"))
expect_equal(as.character(as.bactid("Escherichia coli")), "ESCCOL")
expect_equal(as.character(as.bactid("P. aer")), "PSEAER") # not Pasteurella aerogenes
expect_equal(as.character(as.bactid("Negative rods")), "GNR")
expect_equal(as.character(as.bactid("MRSE")), "STAEPI")
expect_equal(as.character(as.bactid("VRE")), "ENC")
expect_equal(as.character(as.bactid("MRPA")), "PSEAER")
expect_equal(as.character(as.bactid("PISP")), "STCPNE")
expect_equal(as.character(as.bactid("PRSP")), "STCPNE")
expect_equal(as.character(as.bactid("VISP")), "STCPNE")
expect_equal(as.character(as.bactid("VRSP")), "STCPNE")
expect_identical(
as.character(
as.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) %>%
as.bactid() %>%
as.character(),
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) %>%
as.bactid() %>%
as.character())
# unknown results
expect_warning(as.bactid(c("INVALID", "Yeah, unknown")))
# print
expect_output(print(as.bactid(c("ESCCOL", NA))))
# helper function
expect_identical(as.bactid("ESCCOL"),
guess_bactid("ESCCOL"))
})