AMR/tests/testthat/test-guess_bactid.R

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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("P. aer"), "PSEAER") # not Pasteurella aerogenes
expect_equal(guess_bactid("Negative rods"), "GNR")
expect_equal(guess_bactid("MRSE"), "STAEPI")
expect_equal(guess_bactid("VRE"), "ENC")
expect_equal(guess_bactid("MRPA"), "PSEAER")
expect_equal(guess_bactid("PISP"), "STCPNE")
expect_equal(guess_bactid("PRSP"), "STCPNE")
expect_equal(guess_bactid("VISP"), "STCPNE")
expect_equal(guess_bactid("VRSP"), "STCPNE")
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())
})