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AMR/tests/testthat/test-mo.R

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# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Analysis #
# #
# SOURCE #
# https://gitlab.com/msberends/AMR #
# #
# LICENCE #
# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# #
# This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the #
# GNU General Public License version 2.0 (GNU GPL-2), as published by #
# the Free Software Foundation. #
# #
# This R package was created for academic research and was publicly #
# released in the hope that it will be useful, but it comes WITHOUT #
# ANY WARRANTY OR LIABILITY. #
# Visit our website for more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== #
context("mo.R")
test_that("as.mo works", {
library(dplyr)
MOs <- AMR::microorganisms %>% filter(!is.na(mo), nchar(mo) > 3)
expect_identical(as.character(MOs$mo), as.character(as.mo(MOs$mo)))
expect_identical(
as.character(as.mo(c("E. coli", "H. influenzae"))),
c("B_ESCHR_COL", "B_HMPHL_INF"))
expect_equal(as.character(as.mo("Escherichia coli")), "B_ESCHR_COL")
expect_equal(as.character(as.mo("Escherichia coli")), "B_ESCHR_COL")
expect_equal(as.character(as.mo(22242416)), "B_ESCHR_COL")
expect_equal(as.character(as.mo("Escherichia species")), "B_ESCHR")
expect_equal(as.character(as.mo("Escherichia")), "B_ESCHR")
expect_equal(as.character(as.mo("Esch spp.")), "B_ESCHR")
expect_equal(as.character(as.mo(" B_ESCHR_COL ")), "B_ESCHR_COL")
expect_equal(as.character(as.mo("e coli")), "B_ESCHR_COL") # not Campylobacter
expect_equal(as.character(as.mo("klpn")), "B_KLBSL_PNE")
expect_equal(as.character(as.mo("Klebsiella")), "B_KLBSL")
expect_equal(as.character(as.mo("K. pneu rhino")), "B_KLBSL_PNE_RHI") # K. pneumoniae subspp. rhinoscleromatis
expect_equal(as.character(as.mo("Bartonella")), "B_BRTNL")
expect_equal(as.character(as.mo("C. difficile")), "B_CLSTR_DIF")
expect_equal(as.character(as.mo("L. pneumophila")), "B_LGNLL_PNE")
expect_equal(as.character(as.mo("Strepto")), "B_STRPT")
expect_equal(as.character(as.mo("Streptococcus")), "B_STRPT") # not Peptostreptoccus
expect_equal(as.character(as.mo("Estreptococos grupo B")), "B_STRPT_GRB")
expect_equal(as.character(as.mo("Group B Streptococci")), "B_STRPT_GRB")
expect_equal(as.character(as.mo("B_STRPTC")), "B_STRPT") # old MO code (<=v0.5.0)
expect_equal(as.character(as.mo(c("GAS", "GBS"))), c("B_STRPT_GRA", "B_STRPT_GRB"))
expect_equal(as.character(as.mo("S. pyo")), "B_STRPT_PYO") # not Actinomyces pyogenes
# GLIMS
expect_equal(as.character(as.mo("bctfgr")), "B_BCTRD_FRA")
expect_equal(as.character(as.mo("MRSE")), "B_STPHY_EPI")
expect_equal(as.character(as.mo("VRE")), "B_ENTRC")
expect_equal(as.character(as.mo("MRPA")), "B_PSDMN_AER")
expect_equal(as.character(as.mo("PISP")), "B_STRPT_PNE")
expect_equal(as.character(as.mo("PRSP")), "B_STRPT_PNE")
expect_equal(as.character(as.mo("VISP")), "B_STRPT_PNE")
expect_equal(as.character(as.mo("VRSP")), "B_STRPT_PNE")
expect_equal(as.character(as.mo("CNS")), "B_STPHY_CNS")
expect_equal(as.character(as.mo("CoNS")), "B_STPHY_CNS")
expect_equal(as.character(as.mo("CPS")), "B_STPHY_CPS")
expect_equal(as.character(as.mo("CoPS")), "B_STPHY_CPS")
expect_equal(as.character(as.mo(c("Gram negative", "Gram positive"))), c("B_GRAMN", "B_GRAMP"))
# prevalent MO
expect_identical(
suppressWarnings(as.character(
as.mo(c("stau",
"STAU",
"staaur",
"S. aureus",
"S aureus",
"Sthafilokkockus aureeuzz",
"Staphylococcus aureus",
"MRSA",
"VISA")))),
rep("B_STPHY_AUR", 9))
expect_identical(
as.character(
as.mo(c('EHEC', 'EPEC', 'EIEC', 'STEC', 'ATEC', 'UPEC'))),
rep("B_ESCHR_COL", 6))
# unprevalent MO
expect_identical(
as.character(
as.mo(c("burnod",
"B. nodosa",
"B nodosa",
"Burkholderia nodosa"))),
rep("B_BRKHL_NOD", 4))
# empty values
expect_identical(as.character(as.mo(c("", NA, NaN))), rep(NA_character_, 3))
# too few characters
expect_warning(as.mo("ab"))
expect_equal(suppressWarnings(as.character(as.mo(c("Qq species", "", "CRS", "K. pneu rhino", "esco")))),
c("UNKNOWN", NA_character_, "B_STNTR_MAL", "B_KLBSL_PNE_RHI", "B_ESCHR_COL"))
# check for Becker classification
expect_identical(as.character(as.mo("S. epidermidis", Becker = FALSE)), "B_STPHY_EPI")
expect_identical(as.character(as.mo("S. epidermidis", Becker = TRUE)), "B_STPHY_CNS")
expect_identical(as.character(as.mo("STAEPI", Becker = TRUE)), "B_STPHY_CNS")
expect_identical(as.character(as.mo("S. intermedius", Becker = FALSE)), "B_STPHY_INT")
expect_identical(as.character(as.mo("Sta intermedius",Becker = FALSE)), "B_STPHY_INT")
expect_identical(as.character(as.mo("Sta intermedius",Becker = TRUE)), "B_STPHY_CPS")
expect_identical(as.character(as.mo("STAINT", Becker = TRUE)), "B_STPHY_CPS")
# aureus must only be influenced if Becker = "all"
expect_identical(as.character(as.mo("STAAUR", Becker = FALSE)), "B_STPHY_AUR")
expect_identical(as.character(as.mo("STAAUR", Becker = TRUE)), "B_STPHY_AUR")
expect_identical(as.character(as.mo("STAAUR", Becker = "all")), "B_STPHY_CPS")
# check for Lancefield classification
expect_identical(as.character(as.mo("S. pyogenes", Lancefield = FALSE)), "B_STRPT_PYO")
expect_identical(as.character(as.mo("S. pyogenes", Lancefield = TRUE)), "B_STRPT_GRA")
expect_identical(as.character(as.mo("STCPYO", Lancefield = TRUE)), "B_STRPT_GRA") # group A
expect_identical(as.character(as.mo("S. agalactiae", Lancefield = FALSE)), "B_STRPT_AGA")
expect_identical(as.character(as.mo("S. agalactiae", Lancefield = TRUE)), "B_STRPT_GRB") # group B
expect_identical(as.character(suppressWarnings(as.mo("estreptococos grupo B"))), "B_STRPT_GRB")
expect_identical(as.character(as.mo("S. equisimilis", Lancefield = FALSE)), "B_STRPT_DYS_EQU")
expect_identical(as.character(as.mo("S. equisimilis", Lancefield = TRUE)), "B_STRPT_GRC") # group C
# Enterococci must only be influenced if Lancefield = "all"
expect_identical(as.character(as.mo("E. faecium", Lancefield = FALSE)), "B_ENTRC_IUM")
expect_identical(as.character(as.mo("E. faecium", Lancefield = TRUE)), "B_ENTRC_IUM")
expect_identical(as.character(as.mo("E. faecium", Lancefield = "all")), "B_STRPT_GRD") # group D
expect_identical(as.character(as.mo("S. anginosus", Lancefield = FALSE)), "B_STRPT_ANG")
expect_identical(as.character(as.mo("S. anginosus", Lancefield = TRUE)), "B_STRPT_GRF") # group F
expect_identical(as.character(as.mo("S. sanguinis", Lancefield = FALSE)), "B_STRPT_SAN")
expect_identical(as.character(as.mo("S. sanguinis", Lancefield = TRUE)), "B_STRPT_GRH") # group H
expect_identical(as.character(as.mo("S. salivarius", Lancefield = FALSE)), "B_STRPT_SAL")
expect_identical(as.character(as.mo("S. salivarius", Lancefield = TRUE)), "B_STRPT_GRK") # group K
library(dplyr)
# select with one column
expect_identical(
septic_patients[1:10,] %>%
left_join_microorganisms() %>%
select(genus) %>%
as.mo() %>%
as.character(),
c("B_ESCHR", "B_ESCHR", "B_STPHY", "B_STPHY", "B_STPHY",
"B_STPHY", "B_STPHY", "B_STPHY", "B_STPHY", "B_STPHY"))
# select with two columns
expect_identical(
septic_patients[1:10,] %>%
pull(mo),
septic_patients[1:10,] %>%
left_join_microorganisms() %>%
select(genus, species) %>%
as.mo() %>%
as.character())
# unknown results
expect_warning(as.mo(c("INVALID", "Yeah, unknown")))
# too many columns
expect_error(septic_patients %>% select(1:3) %>% as.mo())
# print
expect_output(print(as.mo(c("B_ESCHR_COL", NA))))
# test pull
expect_equal(nrow(septic_patients %>% mutate(mo = as.mo(mo))),
2000)
# test data.frame
expect_equal(nrow(data.frame(test = as.mo("B_ESCHR_COL"))),
1)
# check empty values
expect_equal(as.character(suppressWarnings(as.mo(""))),
NA_character_)
# check less prevalent MOs
expect_equal(as.character(as.mo("Gomphosphaeria aponina delicatula")), "B_GMPHS_APO_DEL")
expect_equal(as.character(as.mo("Gomphosphaeria apo del")), "B_GMPHS_APO_DEL")
expect_equal(as.character(as.mo("G apo deli")), "B_GMPHS_APO_DEL")
expect_equal(as.character(as.mo("Gomphosphaeria aponina")), "B_GMPHS_APO")
expect_equal(as.character(as.mo("Gomphosphaeria species")), "B_GMPHS")
expect_equal(as.character(as.mo("Gomphosphaeria")), "B_GMPHS")
expect_equal(as.character(as.mo(" B_GMPHS_APO ")), "B_GMPHS_APO")
expect_equal(as.character(as.mo("g aponina")), "B_GMPHS_APO")
# check old names
expect_equal(suppressMessages(as.character(as.mo("Escherichia blattae"))), "B_SHMWL_BLA")
print(mo_renamed())
# check uncertain names
expect_equal(suppressWarnings(as.character(as.mo("esco extra_text", allow_uncertain = FALSE))), "UNKNOWN")
expect_equal(suppressWarnings(as.character(as.mo("esco extra_text", allow_uncertain = TRUE))), "B_ESCHR_COL")
expect_warning(as.mo("esco extra_text", allow_uncertain = TRUE))
expect_equal(suppressWarnings(as.character(as.mo("unexisting aureus", allow_uncertain = 3))), "B_STPHY_AUR")
expect_equal(suppressWarnings(as.character(as.mo("unexisting staphy", allow_uncertain = 3))), "B_STPHY")
expect_equal(suppressWarnings(as.character(as.mo("Staphylococcus aureus unexisting", allow_uncertain = 3))), "B_STPHY_AUR")
# predefined reference_df
expect_equal(as.character(as.mo("TestingOwnID",
reference_df = data.frame(mycol = "TestingOwnID", mo = "B_ESCHR_COL"))),
"B_ESCHR_COL")
expect_equal(as.character(as.mo(c("TestingOwnID", "E. coli"),
reference_df = data.frame(mycol = "TestingOwnID", mo = "B_ESCHR_COL"))),
c("B_ESCHR_COL", "B_ESCHR_COL"))
expect_warning(as.mo("TestingOwnID", reference_df = NULL))
expect_error(as.mo("E. coli", reference_df = data.frame(mycol = "TestingOwnID")))
# combination of existing mo and other code
expect_identical(as.character(as.mo(c("B_ESCHR_COL", "ESCCOL"))),
c("B_ESCHR_COL", "B_ESCHR_COL"))
# expect_equal(mo_fullname(c("E. spp.",
# "E. spp",
# "E. species")),
# rep("Escherichia species", 3))
# from different sources
expect_equal(as.character(as.mo(
c("PRTMIR", "bclcer", "B_ESCHR_COL"))),
c("B_PROTS_MIR", "B_BCLLS_CER", "B_ESCHR_COL"))
# hard to find
expect_equal(as.character(suppressWarnings(as.mo(
c("Microbacterium paraoxidans",
"Streptococcus suis (bovis gr)",
"Raoultella (here some text) terrigena")))),
c("B_MCRBC_PAR", "B_STRPT_SUI", "B_RLTLL_TER"))
print(mo_uncertainties())
# Salmonella (City) are all actually Salmonella enterica spp (City)
expect_equal(as.character(suppressMessages(as.mo("Salmonella Goettingen"))),
"B_SLMNL_ENT")
expect_equal(as.character(as.mo("Salmonella Group A")), "B_SLMNL")
# no virusses
expect_warning(as.mo("Virus"))
# summary
expect_equal(length(summary(septic_patients$mo)), 6)
# WHONET codes and NA/NaN
expect_equal(as.character(as.mo(c("xxx", "na", "nan"), debug = TRUE)),
rep(NA_character_, 3))
expect_equal(as.character(as.mo("con")), "UNKNOWN")
expect_equal(as.character(as.mo("xxx")), NA_character_)
expect_equal(as.character(as.mo(c("xxx", "con"))), c(NA_character_, "UNKNOWN"))
expect_equal(as.character(as.mo(c("other", "none", "unknown"))),
rep("UNKNOWN", 3))
expect_null(mo_failures())
expect_true(septic_patients %>% pull(mo) %>% is.mo())
# expect_equal(get_mo_code("test", "mo"), "test")
# expect_equal(length(get_mo_code("Escherichia", "genus")),
# nrow(AMR::microorganisms[base::which(AMR::microorganisms[, "genus"] %in% "Escherichia"),]))
expect_error(translate_allow_uncertain(5))
# very old MO codes (<= v0.5.0)
expect_equal(as.character(as.mo("F_CCCCS_NEO")), "F_CRYPT_NEO")
expect_equal(as.character(as.mo("F_CANDD_GLB")), "F_CANDD_GLA")
})
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