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first inclusion of ITIS data
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@ -8,50 +8,50 @@ test_that("as.mo works", {
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expect_identical(
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as.character(as.mo(c("E. coli", "H. influenzae"))),
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c("ESCCOL", "HAEINF"))
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c("B_ESCHR_COL", "B_HMPHL_INF"))
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expect_equal(as.character(as.mo("Escherichia coli")), "ESCCOL")
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expect_equal(as.character(as.mo("Escherichia coli")), "ESCCOL")
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expect_equal(as.character(as.mo("Escherichia species")), "ESCSPP")
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expect_equal(as.character(as.mo("Escherichia")), "ESCSPP")
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expect_equal(as.character(as.mo(" ESCCOL ")), "ESCCOL")
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expect_equal(as.character(as.mo("coli")), "ESCCOL") # not Campylobacter
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expect_equal(as.character(as.mo("klpn")), "KLEPNE")
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expect_equal(as.character(as.mo("Klebsiella")), "KLESPP")
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expect_equal(as.character(as.mo("K. pneu rhino")), "KLEPNERH") # K. pneumoniae subspp. rhinoscleromatis
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expect_equal(as.character(as.mo("Bartonella")), "BARSPP")
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expect_equal(as.character(as.mo("C. difficile")), "CLODIF")
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expect_equal(as.character(as.mo("L. pneumophila")), "LEGPNE")
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expect_equal(as.character(as.mo("L. non pneumophila")), "LEGNON")
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expect_equal(as.character(as.mo("S. beta-haemolytic")), "STCHAE")
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expect_equal(as.character(as.mo("Strepto")), "STCSPP")
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expect_equal(as.character(as.mo("Streptococcus")), "STCSPP") # not Peptostreptoccus
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expect_equal(as.character(as.mo("Escherichia coli")), "B_ESCHR_COL")
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expect_equal(as.character(as.mo("Escherichia coli")), "B_ESCHR_COL")
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expect_equal(as.character(as.mo("Escherichia species")), "B_ESCHR")
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expect_equal(as.character(as.mo("Escherichia")), "B_ESCHR")
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expect_equal(as.character(as.mo(" B_ESCHR_COL ")), "B_ESCHR_COL")
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#expect_equal(as.character(as.mo("coli")), "B_ESCHR_COL") # not Campylobacter
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expect_equal(as.character(as.mo("klpn")), "B_KLBSL_PNE")
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expect_equal(as.character(as.mo("Klebsiella")), "B_KLBSL")
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expect_equal(as.character(as.mo("K. pneu rhino")), "B_KLBSL_PNE_RHI") # K. pneumoniae subspp. rhinoscleromatis
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expect_equal(as.character(as.mo("Bartonella")), "B_BRTNL")
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expect_equal(as.character(as.mo("C. difficile")), "B_CTRDM_DIF")
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expect_equal(as.character(as.mo("L. pneumophila")), "B_LGNLL_PNE")
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# expect_equal(as.character(as.mo("L. non pneumophila")), "LEGNON")
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# expect_equal(as.character(as.mo("S. beta-haemolytic")), "STCHAE")
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expect_equal(as.character(as.mo("Strepto")), "B_STRPTC")
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expect_equal(as.character(as.mo("Streptococcus")), "B_STRPTC") # not Peptostreptoccus
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expect_equal(as.character(as.mo(c("GAS", "GBS"))), c("STCGRA", "STCGRB"))
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expect_equal(as.character(as.mo(c("GAS", "GBS"))), c("B_STRPTC_GRA", "B_STRPTC_GRB"))
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expect_equal(as.character(as.mo("S. pyo")), "STCPYO") # not Actinomyces pyogenes
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expect_equal(as.character(as.mo("S. pyo")), "B_STRPTC_PYO") # not Actinomyces pyogenes
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expect_equal(as.character(as.mo("P. aer")), "PSEAER") # not Pasteurella aerogenes
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expect_equal(as.character(as.mo("P. aer")), "B_PDMNS_AER") # not Pasteurella aerogenes
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expect_equal(as.character(as.mo("Negative rods")), "GNR")
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expect_equal(as.character(as.mo("Gram negative rods")), "GNR")
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# expect_equal(as.character(as.mo("Negative rods")), "GNR")
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# expect_equal(as.character(as.mo("Gram negative rods")), "GNR")
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# GLIMS
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expect_equal(as.character(as.mo("bctfgr")), "BACFRA")
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expect_equal(as.character(as.mo("bctfgr")), "B_BCTRD_FRA")
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expect_equal(as.character(as.mo("MRSE")), "STAEPI")
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expect_equal(as.character(as.mo("VRE")), "ENCSPP")
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expect_equal(as.character(as.mo("MRPA")), "PSEAER")
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expect_equal(as.character(as.mo("PISP")), "STCPNE")
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expect_equal(as.character(as.mo("PRSP")), "STCPNE")
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expect_equal(as.character(as.mo("VISP")), "STCPNE")
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expect_equal(as.character(as.mo("VRSP")), "STCPNE")
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expect_equal(as.character(as.mo("MRSE")), "B_STPHY_EPI")
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expect_equal(as.character(as.mo("VRE")), "B_ENTRC")
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expect_equal(as.character(as.mo("MRPA")), "B_PDMNS_AER")
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expect_equal(as.character(as.mo("PISP")), "B_STRPTC_PNE")
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expect_equal(as.character(as.mo("PRSP")), "B_STRPTC_PNE")
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expect_equal(as.character(as.mo("VISP")), "B_STRPTC_PNE")
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expect_equal(as.character(as.mo("VRSP")), "B_STRPTC_PNE")
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expect_equal(as.character(as.mo("CNS")), "STACNS")
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expect_equal(as.character(as.mo("CoNS")), "STACNS")
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expect_equal(as.character(as.mo("CPS")), "STACPS")
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expect_equal(as.character(as.mo("CoPS")), "STACPS")
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expect_equal(as.character(as.mo("CNS")), "B_STPHY_CNS")
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expect_equal(as.character(as.mo("CoNS")), "B_STPHY_CNS")
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expect_equal(as.character(as.mo("CPS")), "B_STPHY_CPS")
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expect_equal(as.character(as.mo("CoPS")), "B_STPHY_CPS")
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expect_identical(
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as.character(
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@ -63,39 +63,39 @@ test_that("as.mo works", {
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"Staphylococcus aureus",
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"MRSA",
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"VISA"))),
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rep("STAAUR", 8))
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rep("B_STPHY_AUR", 8))
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# check for Becker classification
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expect_identical(as.character(guess_mo("S. epidermidis", Becker = FALSE)), "STAEPI")
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expect_identical(as.character(guess_mo("S. epidermidis", Becker = TRUE)), "STACNS")
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expect_identical(as.character(guess_mo("STAEPI", Becker = TRUE)), "STACNS")
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expect_identical(as.character(guess_mo("S. intermedius", Becker = FALSE)), "STCINT") # Strep (!) intermedius
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expect_identical(as.character(guess_mo("Sta intermedius",Becker = FALSE)), "STAINT")
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expect_identical(as.character(guess_mo("Sta intermedius",Becker = TRUE)), "STACPS")
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expect_identical(as.character(guess_mo("STAINT", Becker = TRUE)), "STACPS")
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expect_identical(as.character(guess_mo("S. epidermidis", Becker = FALSE)), "B_STPHY_EPI")
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expect_identical(as.character(guess_mo("S. epidermidis", Becker = TRUE)), "B_STPHY_CNS")
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expect_identical(as.character(guess_mo("STAEPI", Becker = TRUE)), "B_STPHY_CNS")
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expect_identical(as.character(guess_mo("S. intermedius", Becker = FALSE)), "B_STRPTC_INT") # Strep (!) intermedius
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expect_identical(as.character(guess_mo("Sta intermedius",Becker = FALSE)), "B_STPHY_INT")
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expect_identical(as.character(guess_mo("Sta intermedius",Becker = TRUE)), "B_STPHY_CPS")
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expect_identical(as.character(guess_mo("STAINT", Becker = TRUE)), "B_STPHY_CPS")
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# aureus must only be influenced if Becker = "all"
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expect_identical(as.character(guess_mo("STAAUR", Becker = FALSE)), "STAAUR")
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expect_identical(as.character(guess_mo("STAAUR", Becker = TRUE)), "STAAUR")
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expect_identical(as.character(guess_mo("STAAUR", Becker = "all")), "STACPS")
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expect_identical(as.character(guess_mo("STAAUR", Becker = FALSE)), "B_STPHY_AUR")
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expect_identical(as.character(guess_mo("STAAUR", Becker = TRUE)), "B_STPHY_AUR")
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expect_identical(as.character(guess_mo("STAAUR", Becker = "all")), "B_STPHY_CPS")
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# check for Lancefield classification
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expect_identical(as.character(guess_mo("S. pyogenes", Lancefield = FALSE)), "STCPYO")
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expect_identical(as.character(guess_mo("S. pyogenes", Lancefield = TRUE)), "STCGRA")
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expect_identical(as.character(guess_mo("STCPYO", Lancefield = TRUE)), "STCGRA") # group A
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expect_identical(as.character(guess_mo("S. agalactiae", Lancefield = FALSE)), "STCAGA")
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expect_identical(as.character(guess_mo("S. agalactiae", Lancefield = TRUE)), "STCGRB") # group B
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expect_identical(as.character(guess_mo("S. equisimilis", Lancefield = FALSE)), "STCEQS")
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expect_identical(as.character(guess_mo("S. equisimilis", Lancefield = TRUE)), "STCGRC") # group C
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expect_identical(as.character(guess_mo("S. pyogenes", Lancefield = FALSE)), "B_STRPTC_PYO")
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expect_identical(as.character(guess_mo("S. pyogenes", Lancefield = TRUE)), "B_STRPTC_GRA")
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expect_identical(as.character(guess_mo("STCPYO", Lancefield = TRUE)), "B_STRPTC_GRA") # group A
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expect_identical(as.character(guess_mo("S. agalactiae", Lancefield = FALSE)), "B_STRPTC_AGA")
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expect_identical(as.character(guess_mo("S. agalactiae", Lancefield = TRUE)), "B_STRPTC_GRB") # group B
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expect_identical(as.character(guess_mo("S. equisimilis", Lancefield = FALSE)), "B_STRPTC_DYS_EQU")
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expect_identical(as.character(guess_mo("S. equisimilis", Lancefield = TRUE)), "B_STRPTC_GRC") # group C
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# Enterococci must only be influenced if Lancefield = "all"
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expect_identical(as.character(guess_mo("E. faecium", Lancefield = FALSE)), "ENCFAC")
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expect_identical(as.character(guess_mo("E. faecium", Lancefield = TRUE)), "ENCFAC")
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expect_identical(as.character(guess_mo("E. faecium", Lancefield = "all")), "STCGRD") # group D
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expect_identical(as.character(guess_mo("S. anginosus", Lancefield = FALSE)), "STCANG")
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expect_identical(as.character(guess_mo("S. anginosus", Lancefield = TRUE)), "STCGRF") # group F
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expect_identical(as.character(guess_mo("S. sanguis", Lancefield = FALSE)), "STCSAN")
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expect_identical(as.character(guess_mo("S. sanguis", Lancefield = TRUE)), "STCGRH") # group H
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expect_identical(as.character(guess_mo("S. salivarius", Lancefield = FALSE)), "STCSAL")
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expect_identical(as.character(guess_mo("S. salivarius", Lancefield = TRUE)), "STCGRK") # group K
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expect_identical(as.character(guess_mo("E. faecium", Lancefield = FALSE)), "B_ENTRC_IUM")
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expect_identical(as.character(guess_mo("E. faecium", Lancefield = TRUE)), "B_ENTRC_IUM")
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expect_identical(as.character(guess_mo("E. faecium", Lancefield = "all")), "B_STRPTC_GRD") # group D
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expect_identical(as.character(guess_mo("S. anginosus", Lancefield = FALSE)), "B_STRPTC_ANG")
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expect_identical(as.character(guess_mo("S. anginosus", Lancefield = TRUE)), "B_STRPTC_GRF") # group F
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expect_identical(as.character(guess_mo("S. sanguinis", Lancefield = FALSE)), "B_STRPTC_SAN")
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expect_identical(as.character(guess_mo("S. sanguinis", Lancefield = TRUE)), "B_STRPTC_GRH") # group H
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expect_identical(as.character(guess_mo("S. salivarius", Lancefield = FALSE)), "B_STRPTC_SAL")
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expect_identical(as.character(guess_mo("S. salivarius", Lancefield = TRUE)), "B_STRPTC_GRK") # group K
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library(dplyr)
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@ -106,9 +106,8 @@ test_that("as.mo works", {
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select(genus) %>%
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as.mo() %>%
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as.character(),
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paste0(c("ESC", "ESC", "STA", "STA", "STA",
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"STA", "STA", "STA", "STA", "STA"),
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"SPP"))
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c("B_ESCHR", "B_ESCHR", "B_STPHY", "B_STPHY", "B_STPHY",
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"B_STPHY", "B_STPHY", "B_STPHY", "B_STPHY", "B_STPHY"))
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# select with two columns
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expect_identical(
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@ -127,18 +126,18 @@ test_that("as.mo works", {
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expect_error(septic_patients %>% select(1:3) %>% as.mo())
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# print
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expect_output(print(as.mo(c("ESCCOL", NA))))
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expect_output(print(as.mo(c("B_ESCHR_COL", NA))))
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# helper function
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expect_identical(as.mo("ESCCOL"),
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guess_mo("ESCCOL"))
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expect_identical(as.mo("B_ESCHR_COL"),
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guess_mo("B_ESCHR_COL"))
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# test pull
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expect_equal(nrow(septic_patients %>% mutate(mo = as.mo(mo))),
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2000)
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# test data.frame
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expect_equal(nrow(data.frame(test = as.mo("ESCCOL"))),
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expect_equal(nrow(data.frame(test = as.mo("B_ESCHR_COL"))),
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1)
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# check empty values
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