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(v0.7.1.9038) mo algorithm inprovements

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dr. M.S. (Matthijs) Berends
2019-08-12 19:07:15 +02:00
parent c44c5e3913
commit 5f2733349e
10 changed files with 226 additions and 130 deletions
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6
tests/testthat/test-mo.R
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@ -197,8 +197,8 @@ test_that("as.mo works", {
print(mo_renamed())
# check uncertain names
expect_equal(suppressWarnings(as.character(as.mo("esco extra_text", allow_uncertain = FALSE))), "UNKNOWN")
expect_equal(suppressWarnings(as.character(as.mo("esco extra_text", allow_uncertain = TRUE))), "B_ESCHR_COL")
expect_equal(suppressWarnings(as.character(as.mo("staaur extratest", allow_uncertain = TRUE))), "B_STPHY_AUR")
expect_equal(suppressWarnings(as.character(as.mo("staaur extratest", allow_uncertain = FALSE))), "UNKNOWN")
expect_warning(as.mo("esco extra_text", allow_uncertain = TRUE))
expect_equal(suppressWarnings(as.character(as.mo("unexisting aureus", allow_uncertain = 3))), "B_STPHY_AUR")
expect_equal(suppressWarnings(as.character(as.mo("unexisting staphy", allow_uncertain = 3))), "B_STPHY")
@ -270,7 +270,7 @@ test_that("as.mo works", {
expect_equal(as.character(as.mo("F_CANDD_GLB")), "F_CANDD_GLA")
# debug mode
expect_output(print(suppressWarnings(as.mo("kshgcjkhsdgkshjdfsfvsdfv", debug = TRUE, allow_uncertain = 3))))
expect_output(print(suppressMessages(suppressWarnings(as.mo("kshgcjkhsdgkshjdfsfvsdfv", debug = TRUE, allow_uncertain = 3)))))
# ..coccus
expect_equal(as.character(as.mo(c("meningococ", "gonococ", "pneumococ"))),