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New mo algorithm, prepare for 2.0
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Dr. Matthijs Berends
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cd2acc4a29
@ -1,12 +1,16 @@
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# ==================================================================== #
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# TITLE #
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# Antimicrobial Resistance (AMR) Data Analysis for R #
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# AMR: An R Package for Working with Antimicrobial Resistance Data #
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# #
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# SOURCE #
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# https://github.com/msberends/AMR #
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# #
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# LICENCE #
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# (c) 2018-2022 Berends MS, Luz CF et al. #
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# CITE AS #
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# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
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# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
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# Data. Journal of Statistical Software, 104(3), 1-31. #
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# doi:10.18637/jss.v104.i03 #
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# #
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# Developed at the University of Groningen, the Netherlands, in #
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# collaboration with non-profit organisations Certe Medical #
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# Diagnostics & Advice, and University Medical Center Groningen. #
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@ -27,7 +31,7 @@ MOs <- subset(microorganisms, !is.na(mo) & nchar(mo) > 3)
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expect_identical(as.character(MOs$mo), as.character(as.mo(MOs$mo)))
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expect_identical(
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as.character(as.mo(c("E. coli", "H. influenzae"))),
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as.character(as.mo(c("E. coli", "H. influenzae"), keep_synonyms = FALSE)),
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c("B_ESCHR_COLI", "B_HMPHL_INFL")
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)
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@ -36,12 +40,12 @@ expect_equal(as.character(as.mo("Escherichia coli")), "B_ESCHR_COLI")
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expect_equal(as.character(as.mo(112283007)), "B_ESCHR_COLI")
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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("Esch spp.")), "B_ESCHR")
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expect_equal(as.character(as.mo("Eschr spp.")), "B_ESCHR")
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expect_equal(as.character(as.mo(" B_ESCHR_COLI ")), "B_ESCHR_COLI")
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expect_equal(as.character(as.mo("e coli")), "B_ESCHR_COLI") # not Campylobacter
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expect_equal(as.character(as.mo("klpn")), "B_KLBSL_PNMN")
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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_PNMN_RHNS") # K. pneumoniae subspp. rhinoscleromatis
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expect_equal(as.character(as.mo("K. pneumo rhino")), "B_KLBSL_PNMN_RHNS") # 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_CRDDS_DFFC")
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expect_equal(as.character(as.mo("L. pneumophila")), "B_LGNLL_PNMP")
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@ -49,9 +53,8 @@ expect_equal(as.character(as.mo("Strepto")), "B_STRPT")
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expect_equal(as.character(as.mo("Streptococcus")), "B_STRPT") # not Peptostreptoccus
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expect_equal(as.character(as.mo("Estreptococos grupo B")), "B_STRPT_GRPB")
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expect_equal(as.character(as.mo("Group B Streptococci")), "B_STRPT_GRPB")
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expect_equal(as.character(as.mo(c("mycobacterie", "mycobakterium"))), c("B_MYCBC", "B_MYCBC"))
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expect_equal(as.character(as.mo(c("GAS", "GBS", "a MGS", "haemoly strep"))), c("B_STRPT_GRPA", "B_STRPT_GRPB", "B_STRPT_MILL", "B_STRPT_HAEM"))
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expect_equal(as.character(as.mo(c("GAS", "GBS", "haemoly strep"))), c("B_STRPT_GRPA", "B_STRPT_GRPB", "B_STRPT_HAEM"))
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expect_equal(as.character(as.mo("S. pyo")), "B_STRPT_PYGN") # not Actinomyces pyogenes
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@ -86,14 +89,13 @@ expect_identical(
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"staaur",
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"S. aureus",
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"S aureus",
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"Sthafilokkockus aureeuzz",
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"Sthafilokkockus aureus",
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"Staphylococcus aureus",
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"MRSA",
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"VISA",
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"meth.-resis. S. aureus (MRSA)"
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))
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"VISA"
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), minimum_matching_score = 0)
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)),
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rep("B_STPHY_AURS", 10)
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rep("B_STPHY_AURS", 9)
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)
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expect_identical(
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as.character(
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@ -144,8 +146,8 @@ expect_identical(as.character(as.mo("STCPYO", Lancefield = TRUE)), "B_STRPT_GRPA
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expect_identical(as.character(as.mo("S. agalactiae", Lancefield = FALSE)), "B_STRPT_AGLC")
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expect_identical(as.character(as.mo("S. agalactiae", Lancefield = TRUE)), "B_STRPT_GRPB") # group B
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expect_identical(as.character(suppressWarnings(as.mo("estreptococos grupo B"))), "B_STRPT_GRPB")
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expect_identical(as.character(as.mo("S. equisimilis", Lancefield = FALSE)), "B_STRPT_DYSG_EQSM")
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expect_identical(as.character(as.mo("S. equisimilis", Lancefield = TRUE)), "B_STRPT_GRPC") # group C
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expect_identical(as.character(as.mo("S. equi", Lancefield = FALSE)), "B_STRPT_EQUI")
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expect_identical(as.character(as.mo("S. equi", Lancefield = TRUE)), "B_STRPT_GRPC") # group C
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# Enterococci must only be influenced if Lancefield = "all"
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expect_identical(as.character(as.mo("E. faecium", Lancefield = FALSE)), "B_ENTRC_FACM")
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expect_identical(as.character(as.mo("E. faecium", Lancefield = TRUE)), "B_ENTRC_FACM")
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@ -209,34 +211,23 @@ expect_equal(
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# check empty values
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expect_equal(
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as.character(suppressWarnings(as.mo(""))),
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as.character(as.mo("")),
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NA_character_
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)
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# check less prevalent MOs
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expect_equal(as.character(as.mo("Gomphosphaeria aponina delicatula")), "B_GMPHS_APNN_DLCT")
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expect_equal(as.character(as.mo("Gomphosphaeria apo del")), "B_GMPHS_APNN_DLCT")
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expect_equal(as.character(as.mo("G apo deli")), "B_GMPHS_APNN_DLCT")
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expect_equal(as.character(as.mo("Gomphosphaeria aponina")), "B_GMPHS_APNN")
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expect_equal(as.character(as.mo("Gomphosphaeria species")), "B_GMPHS")
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expect_equal(as.character(as.mo("Gomphosphaeria")), "B_GMPHS")
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expect_equal(as.character(as.mo(" B_GMPHS_APNN ")), "B_GMPHS_APNN")
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expect_equal(as.character(as.mo("g aponina")), "B_GMPHS_APNN")
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expect_equal(as.character(as.mo("Actinosynnema pretiosum auranticum")), "B_ANNMA_PRTS_ARNT")
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expect_equal(as.character(as.mo("Actinosynnema preti aura")), "B_ANNMA_PRTS_ARNT")
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expect_equal(as.character(as.mo("A pre aur")), "B_ANNMA_PRTS_ARNT")
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expect_equal(as.character(as.mo("Actinosynnema pretiosum")), "B_ANNMA_PRTS")
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expect_equal(as.character(as.mo("Actinosynnema")), "B_ANNMA")
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expect_equal(as.character(as.mo(" B_ANNMA_PRTS ")), "B_ANNMA_PRTS")
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# check old names
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expect_equal(suppressMessages(as.character(as.mo("Escherichia blattae"))), "B_SHMWL_BLTT")
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print(mo_renamed())
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expect_equal(suppressMessages(as.character(as.mo(c("E. coli", "Chlamydo psittaci")))), c("B_ESCHR_COLI", "B_CHLMY_PSTT"))
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expect_equal(suppressMessages(mo_name("eubcom")), "Clostridium combesii")
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# check uncertain names
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expect_equal(suppressMessages(as.character(as.mo("staaur extratest", allow_uncertain = TRUE))), "B_STPHY_AURS")
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expect_equal(suppressWarnings(as.character(as.mo("staaur extratest", allow_uncertain = FALSE))), "UNKNOWN")
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expect_message(as.mo("e coli extra_text", allow_uncertain = TRUE))
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expect_equal(suppressMessages(as.character(as.mo("unexisting aureus", allow_uncertain = 3))), "B_STPHY_AURS")
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expect_equal(suppressMessages(as.character(as.mo("unexisting staphy", allow_uncertain = 3))), "B_STPHY_COPS")
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expect_equal(suppressMessages(as.character(as.mo(c("s aure THISISATEST", "Staphylococcus aureus unexisting"), allow_uncertain = 3))), c("B_STPHY_AURS_AURS", "B_STPHY_AURS_AURS"))
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# predefined reference_df
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expect_equal(
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as.character(as.mo("TestingOwnID",
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@ -255,7 +246,7 @@ expect_error(as.mo("E. coli", reference_df = data.frame(mycol = "TestingOwnID"))
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# combination of existing mo and other code
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expect_identical(
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as.character(as.mo(c("B_ESCHR_COL", "ESCCOL"))),
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suppressWarnings(as.character(as.mo(c("B_ESCHR_COL", "ESCCOL")))),
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c("B_ESCHR_COLI", "B_ESCHR_COLI")
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)
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@ -279,18 +270,18 @@ expect_equal(
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c("B_MCRBC_PRXY", "B_STRPT_SUIS", "B_RLTLL_TRRG")
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)
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expect_stdout(print(mo_uncertainties()))
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x <- as.mo("S. aur")
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x <- as.mo("Sta. aur")
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# many hits
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expect_stdout(print(mo_uncertainties()))
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# Salmonella (City) are all actually Salmonella enterica spp (City)
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expect_equal(
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suppressMessages(as.mo(c("Salmonella Goettingen", "Salmonella Typhimurium", "Salmonella Group A"))),
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suppressMessages(as.mo(c("Salmonella Goettingen", "Salmonella Typhimurium", "Salmonella Group A"), keep_synonyms = FALSE)),
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as.mo(c("Salmonella enterica", "Salmonella enterica", "Salmonella"))
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)
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# no viruses
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expect_equal(as.character(as.mo("Virus")), NA_character_)
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expect_equal(as.mo("Virus"), as.mo("UNKNOWN"))
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# summary
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expect_equal(length(summary(example_isolates$mo)), 6)
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@ -308,13 +299,6 @@ expect_equal(
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rep("UNKNOWN", 3)
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)
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expect_null(mo_failures())
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expect_error(translate_allow_uncertain(5))
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# debug mode
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expect_stdout(print(suppressMessages(suppressWarnings(as.mo("kshgcjkhsdgkshjdfsfvsdfv", debug = TRUE, allow_uncertain = 3)))))
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# ..coccus
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expect_equal(
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as.character(as.mo(c("meningococ", "gonococ", "pneumococ"))),
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