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296 lines
14 KiB
296 lines
14 KiB
# ==================================================================== # |
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# TITLE # |
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# Antimicrobial Resistance (AMR) Data Analysis for R # |
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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) 2018-2021 Berends MS, Luz CF et al. # |
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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"))), |
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c("B_ESCHR_COLI", "B_HMPHL_INFL")) |
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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("Esch 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("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("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("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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# prevalent MO |
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expect_identical( |
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suppressWarnings(as.character( |
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as.mo(c("stau", |
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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 aureeuzz", |
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"Staphylococcus aureus", |
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"MRSA", |
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"VISA")))), |
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rep("B_STPHY_AURS", 9)) |
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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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rep("B_ESCHR_COLI", 6)) |
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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("parnod", |
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"P. nodosa", |
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"P nodosa", |
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"Paraburkholderia nodosa"))), |
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rep("B_PRBRK_NODS", 4)) |
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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(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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# 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. 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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# 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[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("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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example_isolates[1:10, ] %>% |
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pull(mo), |
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example_isolates[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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# 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(nrow(example_isolates %>% mutate(mo = as.mo(mo))), |
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2000) |
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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(nrow(data.frame(test = as.mo("B_ESCHR_COLI"))), |
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1) |
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# check empty values |
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expect_equal(as.character(suppressWarnings(as.mo(""))), |
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NA_character_) |
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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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# 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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# 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 aur THISISATEST", "Staphylococcus aureus unexisting"), allow_uncertain = 3))), c("B_STPHY_AURS_ANRB", "B_STPHY_AURS_ANRB")) |
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# predefined reference_df |
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expect_equal(as.character(as.mo("TestingOwnID", |
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reference_df = data.frame(mycol = "TestingOwnID", mo = "B_ESCHR_COLI"))), |
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"B_ESCHR_COLI") |
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expect_equal(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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c("B_ESCHR_COLI", "B_ESCHR_COLI")) |
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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(as.character(as.mo(c("B_ESCHR_COL", "ESCCOL"))), |
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c("B_ESCHR_COLI", "B_ESCHR_COLI")) |
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# from different sources |
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expect_equal(as.character(as.mo( |
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c("PRTMIR", "bclcer", "B_ESCHR_COLI"))), |
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c("B_PROTS_MRBL", "B_BCLLS_CERS", "B_ESCHR_COLI")) |
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# hard to find |
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expect_equal(as.character(suppressMessages(as.mo( |
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c("Microbacterium paraoxidans", |
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"Streptococcus suis (bovis gr)", |
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"Raoultella (here some text) terrigena")))), |
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c("B_MCRBC_PRXY", "B_STRPT_SUIS", "B_RLTLL_TRRG")) |
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expect_stdout(print(mo_uncertainties())) |
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x <- as.mo("S. 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(suppressMessages(as.mo(c("Salmonella Goettingen", "Salmonella Typhimurium", "Salmonella Group A"))), |
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as.mo(c("Salmonella enterica", "Salmonella enterica", "Salmonella"))) |
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# no virusses |
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expect_equal(as.character(as.mo("Virus")), NA_character_) |
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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(as.character(as.mo(c("xxx", "na", "nan"), debug = TRUE)), |
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rep(NA_character_, 3)) |
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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(as.character(as.mo(c("other", "none", "unknown"))), |
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rep("UNKNOWN", 3)) |
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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(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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# yeasts and fungi |
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expect_equal(suppressWarnings(as.character(as.mo(c("yeasts", "fungi")))), |
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c("F_YEAST", "F_FUNGUS")) |
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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(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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# 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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