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speed improvement for as.mo, more old taxonomic names

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2018-09-27 23:23:48 +02:00
parent 450992baea
commit 2b0080995e
18 changed files with 481 additions and 441 deletions
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5
tests/testthat/test-mo.R
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@ -15,7 +15,7 @@ test_that("as.mo works", {
expect_equal(as.character(as.mo("Escherichia species")), "B_ESCHR")
expect_equal(as.character(as.mo("Escherichia")), "B_ESCHR")
expect_equal(as.character(as.mo(" B_ESCHR_COL ")), "B_ESCHR_COL")
#expect_equal(as.character(as.mo("coli")), "B_ESCHR_COL") # not Campylobacter
expect_equal(as.character(as.mo("e coli")), "B_ESCHR_COL") # not Campylobacter
expect_equal(as.character(as.mo("klpn")), "B_KLBSL_PNE")
expect_equal(as.character(as.mo("Klebsiella")), "B_KLBSL")
expect_equal(as.character(as.mo("K. pneu rhino")), "B_KLBSL_PNE_RHI") # K. pneumoniae subspp. rhinoscleromatis
@ -34,9 +34,6 @@ test_that("as.mo works", {
expect_equal(as.character(as.mo("P. aer")), "B_PDMNS_AER") # not Pasteurella aerogenes
# expect_equal(as.character(as.mo("Negative rods")), "GNR")
# expect_equal(as.character(as.mo("Gram negative rods")), "GNR")
# GLIMS
expect_equal(as.character(as.mo("bctfgr")), "B_BCTRD_FRA")