mirror of https://github.com/msberends/AMR.git
341 lines
13 KiB
R
341 lines
13 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 #
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# https://github.com/msberends/AMR #
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# #
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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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# #
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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://msberends.github.io/AMR/ #
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# ==================================================================== #
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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)))
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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("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("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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# 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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"P. nodosa",
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"P nodosa",
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"Paraburkholderia nodosa"
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))
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),
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rep("B_PRBRK_NODS", 4)
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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_equal(
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suppressWarnings(as.character(as.mo(c("Qq species", "", "CRSM", "K. pneu rhino", "esco")))),
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c("UNKNOWN", NA_character_, "B_STNTR_MLTP", "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")) {
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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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# unknown results
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expect_warning(as.mo(c("INVALID", "Yeah, unknown")))
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# print
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expect_stdout(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 existing mo and other code
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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("B_ESCHR_COLI", "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_RLTLL_TRRG")
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)
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expect_stdout(print(mo_uncertainties()))
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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"), 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(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_equal(
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as.character(as.mo(c("xxx", "na", "nan"), debug = TRUE)),
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rep(NA_character_, 3)
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)
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expect_equal(as.character(as.mo("con")), "UNKNOWN")
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expect_equal(as.character(as.mo("xxx")), NA_character_)
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expect_equal(as.character(as.mo(c("xxx", "con", "eco"))), c(NA_character_, "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("dplyr", min_version = "1.0.0")) {
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# print tibble
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expect_stdout(print(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_equal(
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as.character(as.mo(c("E. coli", "E. coli ignorethis"), ignore_pattern = "this")),
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c("B_ESCHR_COLI", NA)
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)
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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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