mirror of
https://github.com/msberends/AMR.git
synced 2026-11-16 00:10:57 +01:00
dr. M.S. (Matthijs) Berends
179eec584f
The full rebuild of clinical_breakpoints also assigns Salmonella serovars and the Bacteroides fragilis complex correctly and adds ECOFFs for Neocosmospora solani. The rebuilt microorganisms.codes is not included, since it remaps WHONET codes that need review first.
382 lines
16 KiB
R
382 lines
16 KiB
R
# ==================================================================== #
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# TITLE: #
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# AMR: An R Package for Working with Antimicrobial Resistance Data #
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# #
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# SOURCE CODE: #
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# https://github.com/msberends/AMR #
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# #
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# PLEASE CITE THIS SOFTWARE AS: #
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# Berends MS, Luz CF, Friedrich AW, et al. (2022). #
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# AMR: An R Package for Working with Antimicrobial Resistance Data. #
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# Journal of Statistical Software, 104(3), 1-31. #
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# https://doi.org/10.18637/jss.v104.i03 #
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# #
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# Developed at the University of Groningen and the University Medical #
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# Center Groningen in the Netherlands, in collaboration with many #
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# colleagues from around the world, see our website. #
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# #
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# This R package is free software; you can freely use and distribute #
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# it for both personal and commercial purposes under the terms of the #
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# GNU General Public License version 2.0 (GNU GPL-2), as published by #
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# the Free Software Foundation. #
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# We created this package for both routine data analysis and academic #
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# research and it was publicly released in the hope that it will be #
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# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
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# #
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# Visit our website for the full manual and a complete tutorial about #
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# how to conduct AMR data analysis: https://amr-for-r.org #
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# ==================================================================== #
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test_that("test-mo.R", {
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skip_on_cran()
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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, keep_synonyms = TRUE)))
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expect_identical(
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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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expect_equal(as.character(as.mo("Escherichia coli")), "B_ESCHR_COLI")
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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("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. 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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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("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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# GLIMS
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expect_equal(as.character(as.mo("bctfgr")), "B_BCTRD_FRGL")
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expect_equal(as.character(as.mo("MRSE")), "B_STPHY_EPDR")
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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_PSDMN_AERG")
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expect_equal(as.character(as.mo("PISP")), "B_STRPT_PNMN")
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expect_equal(as.character(as.mo("PRSP")), "B_STRPT_PNMN")
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expect_equal(as.character(as.mo("VISP")), "B_STRPT_PNMN")
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expect_equal(as.character(as.mo("VRSP")), "B_STRPT_PNMN")
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expect_equal(as.character(as.mo("CNS")), "B_STPHY_CONS")
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expect_equal(as.character(as.mo("CoNS")), "B_STPHY_CONS")
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expect_equal(as.character(as.mo("CPS")), "B_STPHY_COPS")
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expect_equal(as.character(as.mo("CoPS")), "B_STPHY_COPS")
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expect_equal(as.character(as.mo("VGS")), "B_STRPT_VIRI")
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expect_equal(as.character(as.mo("streptococcus milleri")), "B_STRPT_MILL")
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expect_equal(as.character(as.mo(c("Gram negative", "Gram positive"))), c("B_GRAMN", "B_GRAMP"))
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# expect_warning(as.mo("Acinetobacter calcoaceticus/baumannii complex"))
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# Issue #287: "X complex" fallback to "X" when complex is not a distinct taxon
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expect_identical(as.character(suppressWarnings(as.mo("Proteus vulgaris complex"))), as.character(suppressWarnings(as.mo("Proteus vulgaris"))))
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expect_identical(as.character(suppressWarnings(as.mo("Enterobacter cloacae complex"))), as.character(as.mo("Enterobacter cloacae complex")))
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# a complex named after several of its species returns the complex, not one of the species
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expect_identical(as.character(as.mo(c("Acinetobacter calcoaceticus-baumannii complex", "Acinetobacter calcoaceticus/baumannii complex"))), c("B_ACNTB_BMNN-C", "B_ACNTB_BMNN-C"))
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expect_identical(as.character(as.mo("Klebsiella pneumoniae-variicola complex")), "B_KLBSL_PNMN-C")
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# Issue #288: abbreviated genus with exact species epithet match should win
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expect_identical(
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as.character(suppressWarnings(as.mo("S. apiospermum"))),
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as.character(suppressWarnings(as.mo("Scedosporium apiospermum")))
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)
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# prevalent MO
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expect_identical(
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suppressWarnings(as.character(
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as.mo(c(
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"stau", # WHONET code
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"STAU",
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"staaur",
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"S. aureus",
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"S aureus",
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"Sthafilokkockus aureus", # handles incorrect spelling
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"Staphylococcus aureus (MRSA)",
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"MRSA", # Methicillin Resistant S. aureus
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"VISA", # Vancomycin Intermediate S. aureus
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"VRSA", # Vancomycin Resistant S. aureus
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115329001 # SNOMED CT code
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))
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)),
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rep("B_STPHY_AURS", 11)
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)
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expect_identical(
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as.character(
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as.mo(c("EHEC", "EPEC", "EIEC", "STEC", "ATEC", "UPEC"))
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),
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rep("B_ESCHR_COLI", 6)
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)
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# unprevalent MO
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expect_identical(
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as.character(
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as.mo(c(
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"parnod",
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"Paraburkholderia nodosa"
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))
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),
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rep("B_PRBRK_NODS", 2)
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)
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# empty values
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expect_identical(as.character(as.mo(c("", " ", NA, NaN))), rep(NA_character_, 4))
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expect_identical(as.character(as.mo(" ")), NA_character_)
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# too few characters
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# expect_warning(as.mo("ab"))
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expect_identical(
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suppressWarnings(as.character(as.mo(c("Qq species", "MRSA", "K. pneu rhino", "esco")))),
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c("UNKNOWN", "B_STPHY_AURS", "B_KLBSL_PNMN_RHNS", "B_ESCHR_COLI")
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)
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# check for Becker classification
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expect_identical(as.character(as.mo("S. epidermidis", Becker = FALSE)), "B_STPHY_EPDR")
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expect_identical(as.character(as.mo("S. epidermidis", Becker = TRUE)), "B_STPHY_CONS")
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expect_identical(as.character(as.mo("STAEPI", Becker = TRUE)), "B_STPHY_CONS")
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expect_identical(as.character(as.mo("Sta intermedius", Becker = FALSE)), "B_STPHY_INTR")
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expect_identical(as.character(as.mo("Sta intermedius", Becker = TRUE)), "B_STPHY_COPS")
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expect_identical(as.character(as.mo("STAINT", Becker = TRUE)), "B_STPHY_COPS")
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# aureus must only be influenced if Becker = "all"
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expect_identical(as.character(as.mo("STAAUR", Becker = FALSE)), "B_STPHY_AURS")
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expect_identical(as.character(as.mo("STAAUR", Becker = TRUE)), "B_STPHY_AURS")
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expect_identical(as.character(as.mo("STAAUR", Becker = "all")), "B_STPHY_COPS")
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# check for Lancefield classification
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expect_identical(as.character(as.mo("S. pyogenes", Lancefield = FALSE)), "B_STRPT_PYGN")
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expect_identical(as.character(as.mo("S. pyogenes", Lancefield = TRUE)), "B_STRPT_GRPA")
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expect_identical(as.character(as.mo("STCPYO", Lancefield = TRUE)), "B_STRPT_GRPA") # group A
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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. 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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expect_identical(as.character(as.mo("E. faecium", Lancefield = "all")), "B_STRPT_GRPD") # group D
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expect_identical(as.character(as.mo("S. anginosus", Lancefield = FALSE)), "B_STRPT_ANGN")
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expect_identical(as.character(as.mo("S. anginosus", Lancefield = TRUE)), "B_STRPT_GRPF") # group F
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expect_identical(as.character(as.mo("S. sanguinis", Lancefield = FALSE)), "B_STRPT_SNGN")
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expect_identical(as.character(as.mo("S. sanguinis", Lancefield = TRUE)), "B_STRPT_GRPH") # group H
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expect_identical(as.character(as.mo("S. salivarius", Lancefield = FALSE)), "B_STRPT_SLVR")
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expect_identical(as.character(as.mo("S. salivarius", Lancefield = TRUE)), "B_STRPT_GRPK") # group K
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if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0", also_load = TRUE)) {
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# select with one column
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expect_identical(
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example_isolates %>%
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slice(1:10) %>%
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left_join_microorganisms() %>%
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select(genus) %>%
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as.mo() %>%
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as.character(),
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c(
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"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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)
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)
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# select with two columns
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expect_identical(
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example_isolates %>%
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slice(1:10) %>%
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pull(mo),
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example_isolates %>%
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slice(1:10) %>%
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left_join_microorganisms() %>%
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select(genus, species) %>%
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as.mo()
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)
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# too many columns
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expect_error(example_isolates %>% select(1:3) %>% as.mo())
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# test pull
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expect_equal(
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nrow(example_isolates %>% mutate(mo = as.mo(mo))),
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2000
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)
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expect_true(example_isolates %>% pull(mo) %>% is.mo())
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}
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# print
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expect_output(print(as.mo(c("B_ESCHR_COLI", NA))))
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# test data.frame
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expect_equal(
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nrow(data.frame(test = as.mo("B_ESCHR_COLI"))),
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1
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)
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# check empty values
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expect_equal(
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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("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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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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# predefined reference_df
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expect_equal(
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as.character(as.mo("TestingOwnID",
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reference_df = data.frame(mycol = "TestingOwnID", mo = "B_ESCHR_COLI")
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)),
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"B_ESCHR_COLI"
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)
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expect_equal(
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as.character(as.mo(c("TestingOwnID", "E. coli"),
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reference_df = data.frame(mycol = "TestingOwnID", mo = "B_ESCHR_COLI")
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)),
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c("B_ESCHR_COLI", "B_ESCHR_COLI")
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)
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# # expect_warning(as.mo("TestingOwnID", reference_df = NULL))
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expect_error(as.mo("E. coli", reference_df = data.frame(mycol = "TestingOwnID")))
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# combination of an unknown MO code and other code: MO codes are never guessed (see test-data-microorganisms.R)
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expect_identical(
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suppressWarnings(as.character(as.mo(c("B_ESCHR_COL", "ESCCOL")))),
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c(NA, "B_ESCHR_COLI")
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)
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# from different sources
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expect_equal(
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as.character(as.mo(
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c("PRTMIR", "bclcer", "B_ESCHR_COLI")
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)),
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c("B_PROTS_MRBL", "B_BCLLS_CERS", "B_ESCHR_COLI")
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)
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# hard to find
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expect_equal(
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as.character(suppressMessages(as.mo(
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c(
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"Microbacterium paraoxidans",
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"Streptococcus suis (bovis gr)",
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"Raoultella (here some text) terrigena"
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)
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))),
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c("B_MCRBC_PRXY", "B_STRPT_SUIS", "B_KLBSL_TRRG")
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)
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x <- as.mo("Sta. aur")
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# no viruses
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expect_equal(suppressWarnings(as.mo("Virus")), as.mo("UNKNOWN"))
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# summary
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expect_equal(length(summary(example_isolates$mo)), 6)
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# WHONET codes and NA/NaN
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expect_true(all(is.na(as.mo(c("xxx", "na", "nan")))))
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expect_equal(as.character(as.mo(c("con", "eco"))), c("UNKNOWN", "B_ESCHR_COLI"))
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expect_equal(
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as.character(suppressWarnings(as.mo(c("other", "none", "unknown")))),
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rep("UNKNOWN", 3)
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)
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# ..coccus
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expect_equal(
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as.character(as.mo(c("meningococ", "gonococ", "pneumococ"))),
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c("B_NESSR_MNNG", "B_NESSR_GNRR", "B_STRPT_PNMN")
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)
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# yeasts and fungi
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expect_equal(
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suppressWarnings(as.character(as.mo(c("yeasts", "fungi")))),
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c("F_YEAST", "F_FUNGUS")
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)
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if (AMR:::pkg_is_available("tibble")) {
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# print tibble
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expect_output(print(tibble::tibble(mo = as.mo("B_ESCHR_COLI"))))
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}
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# assigning and subsetting
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x <- example_isolates$mo
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expect_inherits(x[1], "mo")
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expect_inherits(x[[1]], "mo")
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expect_inherits(c(x[1], x[9]), "mo")
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# expect_warning(x[1] <- "invalid code")
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# expect_warning(x[[1]] <- "invalid code")
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# expect_warning(c(x[1], "test"))
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# ignoring patterns
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expect_true(is.na(as.mo("E. coli ignorethis", ignore_pattern = "this")))
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# frequency tables
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if (AMR:::pkg_is_available("cleaner")) {
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expect_inherits(cleaner::freq(example_isolates$mo), "freq")
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}
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# skimr
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if (AMR:::pkg_is_available("skimr", min_version = "2.0.0", also_load = TRUE)) {
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expect_named(
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skim(example_isolates$mo),
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c("skim_type", "skim_variable", "n_missing", "complete_rate", "mo.n_unique", "mo.gram_negative", "mo.gram_positive", "mo.yeast", "mo.top_genus", "mo.top_species")
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)
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}
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# "P. knowlesi" must resolve to Plasmodium knowlesi, not a Pseudomonas species,
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# even though P. knowlesi has subspecies (curtisi, wallikeri) sharing the epithet.
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expect_identical(
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as.mo("P. knowlesi", keep_synonyms = TRUE, info = FALSE),
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as.mo("Plasmodium knowlesi", keep_synonyms = TRUE, info = FALSE)
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)
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expect_identical(
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mo_name("P. knowlesi", keep_synonyms = TRUE, language = NULL),
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"Plasmodium knowlesi"
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)
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# Non-regression: the original #288 example must still work.
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expect_identical(
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mo_genus("S. apiospermum", keep_synonyms = TRUE, language = NULL),
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"Scedosporium"
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)
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# Salmonella serovars written with the species (these returned S. bongori or S. enterica diarizonae until 2026)
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expect_identical(
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as.character(as.mo(c(
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"Salmonella enterica Typhi", "Salmonella enterica serovar Typhi",
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"Salmonella enterica subsp. enterica serovar Typhi", "Salmonella enterica Typhimurium",
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"Salmonella enterica Paratyphi A", "Salmonella grupo B"
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), info = FALSE)),
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c("B_SLMNL_TYPH", "B_SLMNL_TYPH", "B_SLMNL_TYPH", "B_SLMNL_HMRM", "B_SLMNL_PRTA", "B_SLMNL_GRPB")
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)
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expect_identical(as.character(as.mo("Salmonella enterica arizonae", info = FALSE)), "B_SLMNL_ENTR_ARZN")
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# translated names, such as the output of mo_name() in the set language
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translated_mos <- c("B_STPHY_CONS", "B_STPHY_COPS", "B_STRPT_HAEM", "B_STRPT_GRPA", "B_STRPT_GRPB", "B_STRPT_ABCG", "B_STRPT_MILL", "B_STRPT_VIRI", "B_SLMNL_GRPB", "B_GRAMN", "B_GRAMP", "F_YEAST", "F_FUNGUS", "P_PROTOZOAN", "UNKNOWN")
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for (lang in setdiff(AMR:::LANGUAGES_SUPPORTED, "en")) {
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expect_identical(as.character(as.mo(mo_name(translated_mos, language = lang), language = lang, info = FALSE)), translated_mos, info = lang)
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}
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expect_identical(
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as.character(as.mo(c("Staphylocoque à coagulase négative", "Streptocoque Bêta-hémolytique", "streptocoque beta-hemolytique", "Streptococcus groupe A"), language = "fr", info = FALSE)),
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c("B_STPHY_CONS", "B_STRPT_HAEM", "B_STRPT_HAEM", "B_STRPT_GRPA")
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)
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})
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