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more unit tests

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2018-11-02 10:27:57 +01:00
parent e601fd259a
commit 40a159e78d
5 changed files with 87 additions and 89 deletions
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27
tests/testthat/test-mo.R
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@ -22,14 +22,11 @@ test_that("as.mo works", {
expect_equal(as.character(as.mo("Bartonella")), "B_BRTNL")
expect_equal(as.character(as.mo("C. difficile")), "B_CTRDM_DIF")
expect_equal(as.character(as.mo("L. pneumophila")), "B_LGNLL_PNE")
# expect_equal(as.character(as.mo("L. non pneumophila")), "LEGNON")
# expect_equal(as.character(as.mo("S. beta-haemolytic")), "STCHAE")
expect_equal(as.character(as.mo("Strepto")), "B_STRPTC")
expect_equal(as.character(as.mo("Streptococcus")), "B_STRPTC") # not Peptostreptoccus
expect_equal(as.character(as.mo(c("GAS", "GBS"))), c("B_STRPTC_GRA", "B_STRPTC_GRB"))
expect_equal(as.character(as.mo("S. pyo")), "B_STRPTC_PYO") # not Actinomyces pyogenes
expect_equal(as.character(as.mo("P. aer")), "B_PDMNS_AER") # not Pasteurella aerogenes
@ -50,6 +47,9 @@ test_that("as.mo works", {
expect_equal(as.character(as.mo("CPS")), "B_STPHY_CPS")
expect_equal(as.character(as.mo("CoPS")), "B_STPHY_CPS")
expect_equal(as.character(as.mo(c("Gram negative", "Gram positive"))), c("B_GRAMN", "B_GRAMP"))
# prevalent MO
expect_identical(
as.character(
as.mo(c("stau",
@ -61,6 +61,21 @@ test_that("as.mo works", {
"MRSA",
"VISA"))),
rep("B_STPHY_AUR", 8))
# unprevalent MO
expect_identical(
as.character(
as.mo(c("buno",
"BUNO",
"burnod",
"B. nodosa",
"B nodosa",
"Burkholderia nodosa"))),
rep("B_BRKHL_NOD", 6))
# empty values
expect_identical(as.character(as.mo(c("", NA, NaN))), rep(NA_character_, 3))
# too few characters
expect_warning(as.mo("ab"))
# check for Becker classification
expect_identical(as.character(guess_mo("S. epidermidis", Becker = FALSE)), "B_STPHY_EPI")
@ -143,6 +158,7 @@ test_that("as.mo works", {
# check less prevalent MOs
expect_equal(as.character(as.mo("Gomphosphaeria aponina delicatula")), "B_GMPHS_APO_DEL")
expect_equal(as.character(as.mo("Gomphosphaeria apo del")), "B_GMPHS_APO_DEL")
expect_equal(as.character(as.mo("G apo deli")), "B_GMPHS_APO_DEL")
expect_equal(as.character(as.mo("Gomphosphaeria aponina")), "B_GMPHS_APO")
expect_equal(as.character(as.mo("Gomphosphaeria species")), "B_GMPHS")
@ -152,6 +168,11 @@ test_that("as.mo works", {
# check old names
expect_equal(suppressMessages(as.character(as.mo("Escherichia blattae"))), "B_SHMWL_BLA")
# - Didymosphaeria spartinae (unprevalent)
expect_warning(suppressMessages(as.mo("D spartin", allow_uncertain = TRUE)))
# - was renames to Leptosphaeria obiones
expect_equal(suppressWarnings(suppressMessages(as.character(as.mo("D spartin", allow_uncertain = TRUE)))),
"F_LPTSP_OBI")
# check uncertain names
expect_equal(suppressWarnings(as.character(as.mo("esco extra_text", allow_uncertain = FALSE))), NA_character_)