mirror of
https://github.com/msberends/AMR.git
synced 2025-07-10 12:21:53 +02:00
(v2.1.1.9186) replace antibiotics with antimicrobials!
This commit is contained in:
@ -27,294 +27,296 @@
|
||||
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
|
||||
# ==================================================================== #
|
||||
|
||||
MOs <- subset(microorganisms, !is.na(mo) & nchar(mo) > 3)
|
||||
expect_identical(as.character(MOs$mo), as.character(as.mo(MOs$mo, keep_synonyms = TRUE)))
|
||||
test_that("mo works", {
|
||||
MOs <- subset(microorganisms, !is.na(mo) & nchar(mo) > 3)
|
||||
expect_identical(as.character(MOs$mo), as.character(as.mo(MOs$mo, keep_synonyms = TRUE)))
|
||||
|
||||
expect_identical(
|
||||
as.character(as.mo(c("E. coli", "H. influenzae"), keep_synonyms = FALSE)),
|
||||
c("B_ESCHR_COLI", "B_HMPHL_INFL")
|
||||
)
|
||||
|
||||
expect_equal(as.character(as.mo("Escherichia coli")), "B_ESCHR_COLI")
|
||||
expect_equal(as.character(as.mo("Escherichia coli")), "B_ESCHR_COLI")
|
||||
expect_equal(as.character(as.mo(112283007)), "B_ESCHR_COLI")
|
||||
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("Eschr spp.")), "B_ESCHR")
|
||||
expect_equal(as.character(as.mo(" B_ESCHR_COLI ")), "B_ESCHR_COLI")
|
||||
expect_equal(as.character(as.mo("e coli")), "B_ESCHR_COLI") # not Campylobacter
|
||||
expect_equal(as.character(as.mo("klpn")), "B_KLBSL_PNMN")
|
||||
expect_equal(as.character(as.mo("Klebsiella")), "B_KLBSL")
|
||||
expect_equal(as.character(as.mo("K. pneumo rhino")), "B_KLBSL_PNMN_RHNS") # K. pneumoniae subspp. rhinoscleromatis
|
||||
expect_equal(as.character(as.mo("Bartonella")), "B_BRTNL")
|
||||
expect_equal(as.character(as.mo("C. difficile")), "B_CRDDS_DFFC")
|
||||
expect_equal(as.character(as.mo("L. pneumophila")), "B_LGNLL_PNMP")
|
||||
expect_equal(as.character(as.mo("Streptococcus")), "B_STRPT") # not Peptostreptoccus
|
||||
expect_equal(as.character(as.mo("Estreptococos grupo B")), "B_STRPT_GRPB")
|
||||
expect_equal(as.character(as.mo("Group B Streptococci")), "B_STRPT_GRPB")
|
||||
|
||||
expect_equal(as.character(as.mo(c("GAS", "GBS", "haemoly strep"))), c("B_STRPT_GRPA", "B_STRPT_GRPB", "B_STRPT_HAEM"))
|
||||
|
||||
|
||||
expect_equal(as.character(as.mo("S. pyo")), "B_STRPT_PYGN") # not Actinomyces pyogenes
|
||||
|
||||
# GLIMS
|
||||
expect_equal(as.character(as.mo("bctfgr")), "B_BCTRD_FRGL")
|
||||
|
||||
expect_equal(as.character(as.mo("MRSE")), "B_STPHY_EPDR")
|
||||
expect_equal(as.character(as.mo("VRE")), "B_ENTRC")
|
||||
expect_equal(as.character(as.mo("MRPA")), "B_PSDMN_AERG")
|
||||
expect_equal(as.character(as.mo("PISP")), "B_STRPT_PNMN")
|
||||
expect_equal(as.character(as.mo("PRSP")), "B_STRPT_PNMN")
|
||||
expect_equal(as.character(as.mo("VISP")), "B_STRPT_PNMN")
|
||||
expect_equal(as.character(as.mo("VRSP")), "B_STRPT_PNMN")
|
||||
|
||||
expect_equal(as.character(as.mo("CNS")), "B_STPHY_CONS")
|
||||
expect_equal(as.character(as.mo("CoNS")), "B_STPHY_CONS")
|
||||
expect_equal(as.character(as.mo("CPS")), "B_STPHY_COPS")
|
||||
expect_equal(as.character(as.mo("CoPS")), "B_STPHY_COPS")
|
||||
expect_equal(as.character(as.mo("VGS")), "B_STRPT_VIRI")
|
||||
expect_equal(as.character(as.mo("streptococcus milleri")), "B_STRPT_MILL")
|
||||
|
||||
|
||||
expect_equal(as.character(as.mo(c("Gram negative", "Gram positive"))), c("B_GRAMN", "B_GRAMP"))
|
||||
|
||||
# expect_warning(as.mo("Acinetobacter calcoaceticus/baumannii complex"))
|
||||
|
||||
# prevalent MO
|
||||
expect_identical(
|
||||
suppressWarnings(as.character(
|
||||
as.mo(c(
|
||||
"stau", # WHONET code
|
||||
"STAU",
|
||||
"staaur",
|
||||
"S. aureus",
|
||||
"S aureus",
|
||||
"Sthafilokkockus aureus", # handles incorrect spelling
|
||||
"Staphylococcus aureus (MRSA)",
|
||||
"MRSA", # Methicillin Resistant S. aureus
|
||||
"VISA", # Vancomycin Intermediate S. aureus
|
||||
"VRSA", # Vancomycin Resistant S. aureus
|
||||
115329001 # SNOMED CT code
|
||||
))
|
||||
)),
|
||||
rep("B_STPHY_AURS", 11)
|
||||
)
|
||||
expect_identical(
|
||||
as.character(
|
||||
as.mo(c("EHEC", "EPEC", "EIEC", "STEC", "ATEC", "UPEC"))
|
||||
),
|
||||
rep("B_ESCHR_COLI", 6)
|
||||
)
|
||||
# unprevalent MO
|
||||
expect_identical(
|
||||
as.character(
|
||||
as.mo(c(
|
||||
"parnod",
|
||||
"Paraburkholderia nodosa"
|
||||
))
|
||||
),
|
||||
rep("B_PRBRK_NODS", 2)
|
||||
)
|
||||
|
||||
# empty values
|
||||
expect_identical(as.character(as.mo(c("", " ", NA, NaN))), rep(NA_character_, 4))
|
||||
expect_identical(as.character(as.mo(" ")), NA_character_)
|
||||
# too few characters
|
||||
# expect_warning(as.mo("ab"))
|
||||
|
||||
expect_identical(
|
||||
suppressWarnings(as.character(as.mo(c("Qq species", "MRSA", "K. pneu rhino", "esco")))),
|
||||
c("UNKNOWN", "B_STPHY_AURS", "B_KLBSL_PNMN_RHNS", "B_ESCHR_COLI")
|
||||
)
|
||||
|
||||
# check for Becker classification
|
||||
expect_identical(as.character(as.mo("S. epidermidis", Becker = FALSE)), "B_STPHY_EPDR")
|
||||
expect_identical(as.character(as.mo("S. epidermidis", Becker = TRUE)), "B_STPHY_CONS")
|
||||
expect_identical(as.character(as.mo("STAEPI", Becker = TRUE)), "B_STPHY_CONS")
|
||||
expect_identical(as.character(as.mo("Sta intermedius", Becker = FALSE)), "B_STPHY_INTR")
|
||||
expect_identical(as.character(as.mo("Sta intermedius", Becker = TRUE)), "B_STPHY_COPS")
|
||||
expect_identical(as.character(as.mo("STAINT", Becker = TRUE)), "B_STPHY_COPS")
|
||||
# aureus must only be influenced if Becker = "all"
|
||||
expect_identical(as.character(as.mo("STAAUR", Becker = FALSE)), "B_STPHY_AURS")
|
||||
expect_identical(as.character(as.mo("STAAUR", Becker = TRUE)), "B_STPHY_AURS")
|
||||
expect_identical(as.character(as.mo("STAAUR", Becker = "all")), "B_STPHY_COPS")
|
||||
|
||||
# check for Lancefield classification
|
||||
expect_identical(as.character(as.mo("S. pyogenes", Lancefield = FALSE)), "B_STRPT_PYGN")
|
||||
expect_identical(as.character(as.mo("S. pyogenes", Lancefield = TRUE)), "B_STRPT_GRPA")
|
||||
expect_identical(as.character(as.mo("STCPYO", Lancefield = TRUE)), "B_STRPT_GRPA") # group A
|
||||
expect_identical(as.character(as.mo("S. agalactiae", Lancefield = FALSE)), "B_STRPT_AGLC")
|
||||
expect_identical(as.character(as.mo("S. agalactiae", Lancefield = TRUE)), "B_STRPT_GRPB") # group B
|
||||
expect_identical(as.character(suppressWarnings(as.mo("estreptococos grupo B"))), "B_STRPT_GRPB")
|
||||
expect_identical(as.character(as.mo("S. equi", Lancefield = FALSE)), "B_STRPT_EQUI")
|
||||
expect_identical(as.character(as.mo("S. equi", Lancefield = TRUE)), "B_STRPT_GRPC") # group C
|
||||
# Enterococci must only be influenced if Lancefield = "all"
|
||||
expect_identical(as.character(as.mo("E. faecium", Lancefield = FALSE)), "B_ENTRC_FACM")
|
||||
expect_identical(as.character(as.mo("E. faecium", Lancefield = TRUE)), "B_ENTRC_FACM")
|
||||
expect_identical(as.character(as.mo("E. faecium", Lancefield = "all")), "B_STRPT_GRPD") # group D
|
||||
expect_identical(as.character(as.mo("S. anginosus", Lancefield = FALSE)), "B_STRPT_ANGN")
|
||||
expect_identical(as.character(as.mo("S. anginosus", Lancefield = TRUE)), "B_STRPT_GRPF") # group F
|
||||
expect_identical(as.character(as.mo("S. sanguinis", Lancefield = FALSE)), "B_STRPT_SNGN")
|
||||
expect_identical(as.character(as.mo("S. sanguinis", Lancefield = TRUE)), "B_STRPT_GRPH") # group H
|
||||
expect_identical(as.character(as.mo("S. salivarius", Lancefield = FALSE)), "B_STRPT_SLVR")
|
||||
expect_identical(as.character(as.mo("S. salivarius", Lancefield = TRUE)), "B_STRPT_GRPK") # group K
|
||||
|
||||
if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0", also_load = TRUE)) {
|
||||
# select with one column
|
||||
expect_identical(
|
||||
example_isolates %>%
|
||||
slice(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"
|
||||
as.character(as.mo(c("E. coli", "H. influenzae"), keep_synonyms = FALSE)),
|
||||
c("B_ESCHR_COLI", "B_HMPHL_INFL")
|
||||
)
|
||||
|
||||
expect_equal(as.character(as.mo("Escherichia coli")), "B_ESCHR_COLI")
|
||||
expect_equal(as.character(as.mo("Escherichia coli")), "B_ESCHR_COLI")
|
||||
expect_equal(as.character(as.mo(112283007)), "B_ESCHR_COLI")
|
||||
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("Eschr spp.")), "B_ESCHR")
|
||||
expect_equal(as.character(as.mo(" B_ESCHR_COLI ")), "B_ESCHR_COLI")
|
||||
expect_equal(as.character(as.mo("e coli")), "B_ESCHR_COLI") # not Campylobacter
|
||||
expect_equal(as.character(as.mo("klpn")), "B_KLBSL_PNMN")
|
||||
expect_equal(as.character(as.mo("Klebsiella")), "B_KLBSL")
|
||||
expect_equal(as.character(as.mo("K. pneumo rhino")), "B_KLBSL_PNMN_RHNS") # K. pneumoniae subspp. rhinoscleromatis
|
||||
expect_equal(as.character(as.mo("Bartonella")), "B_BRTNL")
|
||||
expect_equal(as.character(as.mo("C. difficile")), "B_CRDDS_DFFC")
|
||||
expect_equal(as.character(as.mo("L. pneumophila")), "B_LGNLL_PNMP")
|
||||
expect_equal(as.character(as.mo("Streptococcus")), "B_STRPT") # not Peptostreptoccus
|
||||
expect_equal(as.character(as.mo("Estreptococos grupo B")), "B_STRPT_GRPB")
|
||||
expect_equal(as.character(as.mo("Group B Streptococci")), "B_STRPT_GRPB")
|
||||
|
||||
expect_equal(as.character(as.mo(c("GAS", "GBS", "haemoly strep"))), c("B_STRPT_GRPA", "B_STRPT_GRPB", "B_STRPT_HAEM"))
|
||||
|
||||
|
||||
expect_equal(as.character(as.mo("S. pyo")), "B_STRPT_PYGN") # not Actinomyces pyogenes
|
||||
|
||||
# GLIMS
|
||||
expect_equal(as.character(as.mo("bctfgr")), "B_BCTRD_FRGL")
|
||||
|
||||
expect_equal(as.character(as.mo("MRSE")), "B_STPHY_EPDR")
|
||||
expect_equal(as.character(as.mo("VRE")), "B_ENTRC")
|
||||
expect_equal(as.character(as.mo("MRPA")), "B_PSDMN_AERG")
|
||||
expect_equal(as.character(as.mo("PISP")), "B_STRPT_PNMN")
|
||||
expect_equal(as.character(as.mo("PRSP")), "B_STRPT_PNMN")
|
||||
expect_equal(as.character(as.mo("VISP")), "B_STRPT_PNMN")
|
||||
expect_equal(as.character(as.mo("VRSP")), "B_STRPT_PNMN")
|
||||
|
||||
expect_equal(as.character(as.mo("CNS")), "B_STPHY_CONS")
|
||||
expect_equal(as.character(as.mo("CoNS")), "B_STPHY_CONS")
|
||||
expect_equal(as.character(as.mo("CPS")), "B_STPHY_COPS")
|
||||
expect_equal(as.character(as.mo("CoPS")), "B_STPHY_COPS")
|
||||
expect_equal(as.character(as.mo("VGS")), "B_STRPT_VIRI")
|
||||
expect_equal(as.character(as.mo("streptococcus milleri")), "B_STRPT_MILL")
|
||||
|
||||
|
||||
expect_equal(as.character(as.mo(c("Gram negative", "Gram positive"))), c("B_GRAMN", "B_GRAMP"))
|
||||
|
||||
# expect_warning(as.mo("Acinetobacter calcoaceticus/baumannii complex"))
|
||||
|
||||
# prevalent MO
|
||||
expect_identical(
|
||||
suppressWarnings(as.character(
|
||||
as.mo(c(
|
||||
"stau", # WHONET code
|
||||
"STAU",
|
||||
"staaur",
|
||||
"S. aureus",
|
||||
"S aureus",
|
||||
"Sthafilokkockus aureus", # handles incorrect spelling
|
||||
"Staphylococcus aureus (MRSA)",
|
||||
"MRSA", # Methicillin Resistant S. aureus
|
||||
"VISA", # Vancomycin Intermediate S. aureus
|
||||
"VRSA", # Vancomycin Resistant S. aureus
|
||||
115329001 # SNOMED CT code
|
||||
))
|
||||
)),
|
||||
rep("B_STPHY_AURS", 11)
|
||||
)
|
||||
expect_identical(
|
||||
as.character(
|
||||
as.mo(c("EHEC", "EPEC", "EIEC", "STEC", "ATEC", "UPEC"))
|
||||
),
|
||||
rep("B_ESCHR_COLI", 6)
|
||||
)
|
||||
# unprevalent MO
|
||||
expect_identical(
|
||||
as.character(
|
||||
as.mo(c(
|
||||
"parnod",
|
||||
"Paraburkholderia nodosa"
|
||||
))
|
||||
),
|
||||
rep("B_PRBRK_NODS", 2)
|
||||
)
|
||||
|
||||
# empty values
|
||||
expect_identical(as.character(as.mo(c("", " ", NA, NaN))), rep(NA_character_, 4))
|
||||
expect_identical(as.character(as.mo(" ")), NA_character_)
|
||||
# too few characters
|
||||
# expect_warning(as.mo("ab"))
|
||||
|
||||
expect_identical(
|
||||
suppressWarnings(as.character(as.mo(c("Qq species", "MRSA", "K. pneu rhino", "esco")))),
|
||||
c("UNKNOWN", "B_STPHY_AURS", "B_KLBSL_PNMN_RHNS", "B_ESCHR_COLI")
|
||||
)
|
||||
|
||||
# check for Becker classification
|
||||
expect_identical(as.character(as.mo("S. epidermidis", Becker = FALSE)), "B_STPHY_EPDR")
|
||||
expect_identical(as.character(as.mo("S. epidermidis", Becker = TRUE)), "B_STPHY_CONS")
|
||||
expect_identical(as.character(as.mo("STAEPI", Becker = TRUE)), "B_STPHY_CONS")
|
||||
expect_identical(as.character(as.mo("Sta intermedius", Becker = FALSE)), "B_STPHY_INTR")
|
||||
expect_identical(as.character(as.mo("Sta intermedius", Becker = TRUE)), "B_STPHY_COPS")
|
||||
expect_identical(as.character(as.mo("STAINT", Becker = TRUE)), "B_STPHY_COPS")
|
||||
# aureus must only be influenced if Becker = "all"
|
||||
expect_identical(as.character(as.mo("STAAUR", Becker = FALSE)), "B_STPHY_AURS")
|
||||
expect_identical(as.character(as.mo("STAAUR", Becker = TRUE)), "B_STPHY_AURS")
|
||||
expect_identical(as.character(as.mo("STAAUR", Becker = "all")), "B_STPHY_COPS")
|
||||
|
||||
# check for Lancefield classification
|
||||
expect_identical(as.character(as.mo("S. pyogenes", Lancefield = FALSE)), "B_STRPT_PYGN")
|
||||
expect_identical(as.character(as.mo("S. pyogenes", Lancefield = TRUE)), "B_STRPT_GRPA")
|
||||
expect_identical(as.character(as.mo("STCPYO", Lancefield = TRUE)), "B_STRPT_GRPA") # group A
|
||||
expect_identical(as.character(as.mo("S. agalactiae", Lancefield = FALSE)), "B_STRPT_AGLC")
|
||||
expect_identical(as.character(as.mo("S. agalactiae", Lancefield = TRUE)), "B_STRPT_GRPB") # group B
|
||||
expect_identical(as.character(suppressWarnings(as.mo("estreptococos grupo B"))), "B_STRPT_GRPB")
|
||||
expect_identical(as.character(as.mo("S. equi", Lancefield = FALSE)), "B_STRPT_EQUI")
|
||||
expect_identical(as.character(as.mo("S. equi", Lancefield = TRUE)), "B_STRPT_GRPC") # group C
|
||||
# Enterococci must only be influenced if Lancefield = "all"
|
||||
expect_identical(as.character(as.mo("E. faecium", Lancefield = FALSE)), "B_ENTRC_FACM")
|
||||
expect_identical(as.character(as.mo("E. faecium", Lancefield = TRUE)), "B_ENTRC_FACM")
|
||||
expect_identical(as.character(as.mo("E. faecium", Lancefield = "all")), "B_STRPT_GRPD") # group D
|
||||
expect_identical(as.character(as.mo("S. anginosus", Lancefield = FALSE)), "B_STRPT_ANGN")
|
||||
expect_identical(as.character(as.mo("S. anginosus", Lancefield = TRUE)), "B_STRPT_GRPF") # group F
|
||||
expect_identical(as.character(as.mo("S. sanguinis", Lancefield = FALSE)), "B_STRPT_SNGN")
|
||||
expect_identical(as.character(as.mo("S. sanguinis", Lancefield = TRUE)), "B_STRPT_GRPH") # group H
|
||||
expect_identical(as.character(as.mo("S. salivarius", Lancefield = FALSE)), "B_STRPT_SLVR")
|
||||
expect_identical(as.character(as.mo("S. salivarius", Lancefield = TRUE)), "B_STRPT_GRPK") # group K
|
||||
|
||||
if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0", also_load = TRUE)) {
|
||||
# select with one column
|
||||
expect_identical(
|
||||
example_isolates %>%
|
||||
slice(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(
|
||||
example_isolates %>%
|
||||
slice(1:10) %>%
|
||||
pull(mo),
|
||||
example_isolates %>%
|
||||
slice(1:10) %>%
|
||||
left_join_microorganisms() %>%
|
||||
select(genus, species) %>%
|
||||
as.mo()
|
||||
)
|
||||
# select with two columns
|
||||
expect_identical(
|
||||
example_isolates %>%
|
||||
slice(1:10) %>%
|
||||
pull(mo),
|
||||
example_isolates %>%
|
||||
slice(1:10) %>%
|
||||
left_join_microorganisms() %>%
|
||||
select(genus, species) %>%
|
||||
as.mo()
|
||||
)
|
||||
|
||||
# too many columns
|
||||
expect_error(example_isolates %>% select(1:3) %>% as.mo())
|
||||
# too many columns
|
||||
expect_error(example_isolates %>% select(1:3) %>% as.mo())
|
||||
|
||||
# test pull
|
||||
# test pull
|
||||
expect_equal(
|
||||
nrow(example_isolates %>% mutate(mo = as.mo(mo))),
|
||||
2000
|
||||
)
|
||||
expect_true(example_isolates %>% pull(mo) %>% is.mo())
|
||||
}
|
||||
|
||||
# print
|
||||
expect_output(print(as.mo(c("B_ESCHR_COLI", NA))))
|
||||
|
||||
# test data.frame
|
||||
expect_equal(
|
||||
nrow(example_isolates %>% mutate(mo = as.mo(mo))),
|
||||
2000
|
||||
nrow(data.frame(test = as.mo("B_ESCHR_COLI"))),
|
||||
1
|
||||
)
|
||||
expect_true(example_isolates %>% pull(mo) %>% is.mo())
|
||||
}
|
||||
|
||||
# print
|
||||
expect_stdout(print(as.mo(c("B_ESCHR_COLI", NA))))
|
||||
# check empty values
|
||||
expect_equal(
|
||||
as.character(as.mo("")),
|
||||
NA_character_
|
||||
)
|
||||
|
||||
# test data.frame
|
||||
expect_equal(
|
||||
nrow(data.frame(test = as.mo("B_ESCHR_COLI"))),
|
||||
1
|
||||
)
|
||||
# check less prevalent MOs
|
||||
expect_equal(as.character(as.mo("Actinosynnema pretiosum auranticum")), "B_ANNMA_PRTS_ARNT")
|
||||
# expect_equal(as.character(as.mo("Actinosynnema preti aura")), "B_ANNMA_PRTS_ARNT")
|
||||
# expect_equal(as.character(as.mo("A pre aur")), "B_ANNMA_PRTS_ARNT")
|
||||
expect_equal(as.character(as.mo("Actinosynnema pretiosum")), "B_ANNMA_PRTS")
|
||||
expect_equal(as.character(as.mo("Actinosynnema")), "B_ANNMA")
|
||||
expect_equal(as.character(as.mo(" B_ANNMA_PRTS ")), "B_ANNMA_PRTS")
|
||||
|
||||
# check empty values
|
||||
expect_equal(
|
||||
as.character(as.mo("")),
|
||||
NA_character_
|
||||
)
|
||||
# check old names
|
||||
expect_equal(suppressMessages(as.character(as.mo("Escherichia blattae"))), "B_SHMWL_BLTT")
|
||||
expect_equal(suppressMessages(as.character(as.mo(c("E. coli", "Chlamydo psittaci")))), c("B_ESCHR_COLI", "B_CHLMY_PSTT"))
|
||||
expect_equal(suppressMessages(mo_name("eubcom")), "Clostridium combesii")
|
||||
|
||||
# check less prevalent MOs
|
||||
expect_equal(as.character(as.mo("Actinosynnema pretiosum auranticum")), "B_ANNMA_PRTS_ARNT")
|
||||
# expect_equal(as.character(as.mo("Actinosynnema preti aura")), "B_ANNMA_PRTS_ARNT")
|
||||
# expect_equal(as.character(as.mo("A pre aur")), "B_ANNMA_PRTS_ARNT")
|
||||
expect_equal(as.character(as.mo("Actinosynnema pretiosum")), "B_ANNMA_PRTS")
|
||||
expect_equal(as.character(as.mo("Actinosynnema")), "B_ANNMA")
|
||||
expect_equal(as.character(as.mo(" B_ANNMA_PRTS ")), "B_ANNMA_PRTS")
|
||||
# predefined reference_df
|
||||
expect_equal(
|
||||
as.character(as.mo("TestingOwnID",
|
||||
reference_df = data.frame(mycol = "TestingOwnID", mo = "B_ESCHR_COLI")
|
||||
)),
|
||||
"B_ESCHR_COLI"
|
||||
)
|
||||
expect_equal(
|
||||
as.character(as.mo(c("TestingOwnID", "E. coli"),
|
||||
reference_df = data.frame(mycol = "TestingOwnID", mo = "B_ESCHR_COLI")
|
||||
)),
|
||||
c("B_ESCHR_COLI", "B_ESCHR_COLI")
|
||||
)
|
||||
# # expect_warning(as.mo("TestingOwnID", reference_df = NULL))
|
||||
expect_error(as.mo("E. coli", reference_df = data.frame(mycol = "TestingOwnID")))
|
||||
|
||||
# check old names
|
||||
expect_equal(suppressMessages(as.character(as.mo("Escherichia blattae"))), "B_SHMWL_BLTT")
|
||||
expect_equal(suppressMessages(as.character(as.mo(c("E. coli", "Chlamydo psittaci")))), c("B_ESCHR_COLI", "B_CHLMY_PSTT"))
|
||||
expect_equal(suppressMessages(mo_name("eubcom")), "Clostridium combesii")
|
||||
# combination of existing mo and other code
|
||||
expect_identical(
|
||||
suppressWarnings(as.character(as.mo(c("B_ESCHR_COL", "ESCCOL")))),
|
||||
c("B_ESCHR_COLI", "B_ESCHR_COLI")
|
||||
)
|
||||
|
||||
# predefined reference_df
|
||||
expect_equal(
|
||||
as.character(as.mo("TestingOwnID",
|
||||
reference_df = data.frame(mycol = "TestingOwnID", mo = "B_ESCHR_COLI")
|
||||
)),
|
||||
"B_ESCHR_COLI"
|
||||
)
|
||||
expect_equal(
|
||||
as.character(as.mo(c("TestingOwnID", "E. coli"),
|
||||
reference_df = data.frame(mycol = "TestingOwnID", mo = "B_ESCHR_COLI")
|
||||
)),
|
||||
c("B_ESCHR_COLI", "B_ESCHR_COLI")
|
||||
)
|
||||
# # expect_warning(as.mo("TestingOwnID", reference_df = NULL))
|
||||
expect_error(as.mo("E. coli", reference_df = data.frame(mycol = "TestingOwnID")))
|
||||
# from different sources
|
||||
expect_equal(
|
||||
as.character(as.mo(
|
||||
c("PRTMIR", "bclcer", "B_ESCHR_COLI")
|
||||
)),
|
||||
c("B_PROTS_MRBL", "B_BCLLS_CERS", "B_ESCHR_COLI")
|
||||
)
|
||||
|
||||
# combination of existing mo and other code
|
||||
expect_identical(
|
||||
suppressWarnings(as.character(as.mo(c("B_ESCHR_COL", "ESCCOL")))),
|
||||
c("B_ESCHR_COLI", "B_ESCHR_COLI")
|
||||
)
|
||||
# hard to find
|
||||
expect_equal(
|
||||
as.character(suppressMessages(as.mo(
|
||||
c(
|
||||
"Microbacterium paraoxidans",
|
||||
"Streptococcus suis (bovis gr)",
|
||||
"Raoultella (here some text) terrigena"
|
||||
)
|
||||
))),
|
||||
c("B_MCRBC_PRXY", "B_STRPT_SUIS", "B_KLBSL_TRRG")
|
||||
)
|
||||
expect_output(print(mo_uncertainties()))
|
||||
x <- as.mo("Sta. aur")
|
||||
# many hits
|
||||
expect_output(print(mo_uncertainties()))
|
||||
|
||||
# from different sources
|
||||
expect_equal(
|
||||
as.character(as.mo(
|
||||
c("PRTMIR", "bclcer", "B_ESCHR_COLI")
|
||||
)),
|
||||
c("B_PROTS_MRBL", "B_BCLLS_CERS", "B_ESCHR_COLI")
|
||||
)
|
||||
# no viruses
|
||||
expect_equal(suppressWarnings(as.mo("Virus")), as.mo("UNKNOWN"))
|
||||
|
||||
# hard to find
|
||||
expect_equal(
|
||||
as.character(suppressMessages(as.mo(
|
||||
c(
|
||||
"Microbacterium paraoxidans",
|
||||
"Streptococcus suis (bovis gr)",
|
||||
"Raoultella (here some text) terrigena"
|
||||
)
|
||||
))),
|
||||
c("B_MCRBC_PRXY", "B_STRPT_SUIS", "B_KLBSL_TRRG")
|
||||
)
|
||||
expect_stdout(print(mo_uncertainties()))
|
||||
x <- as.mo("Sta. aur")
|
||||
# many hits
|
||||
expect_stdout(print(mo_uncertainties()))
|
||||
# summary
|
||||
expect_equal(length(summary(example_isolates$mo)), 6)
|
||||
|
||||
# no viruses
|
||||
expect_equal(suppressWarnings(as.mo("Virus")), as.mo("UNKNOWN"))
|
||||
# WHONET codes and NA/NaN
|
||||
expect_true(all(is.na(as.mo(c("xxx", "na", "nan")))))
|
||||
expect_equal(as.character(as.mo(c("con", "eco"))), c("UNKNOWN", "B_ESCHR_COLI"))
|
||||
expect_equal(
|
||||
as.character(suppressWarnings(as.mo(c("other", "none", "unknown")))),
|
||||
rep("UNKNOWN", 3)
|
||||
)
|
||||
|
||||
# summary
|
||||
expect_equal(length(summary(example_isolates$mo)), 6)
|
||||
# ..coccus
|
||||
expect_equal(
|
||||
as.character(as.mo(c("meningococ", "gonococ", "pneumococ"))),
|
||||
c("B_NESSR_MNNG", "B_NESSR_GNRR", "B_STRPT_PNMN")
|
||||
)
|
||||
# yeasts and fungi
|
||||
expect_equal(
|
||||
suppressWarnings(as.character(as.mo(c("yeasts", "fungi")))),
|
||||
c("F_YEAST", "F_FUNGUS")
|
||||
)
|
||||
|
||||
# WHONET codes and NA/NaN
|
||||
expect_true(all(is.na(as.mo(c("xxx", "na", "nan")))))
|
||||
expect_equal(as.character(as.mo(c("con", "eco"))), c("UNKNOWN", "B_ESCHR_COLI"))
|
||||
expect_equal(
|
||||
as.character(suppressWarnings(as.mo(c("other", "none", "unknown")))),
|
||||
rep("UNKNOWN", 3)
|
||||
)
|
||||
if (AMR:::pkg_is_available("tibble")) {
|
||||
# print tibble
|
||||
expect_output(print(tibble::tibble(mo = as.mo("B_ESCHR_COLI"))))
|
||||
}
|
||||
|
||||
# ..coccus
|
||||
expect_equal(
|
||||
as.character(as.mo(c("meningococ", "gonococ", "pneumococ"))),
|
||||
c("B_NESSR_MNNG", "B_NESSR_GNRR", "B_STRPT_PNMN")
|
||||
)
|
||||
# yeasts and fungi
|
||||
expect_equal(
|
||||
suppressWarnings(as.character(as.mo(c("yeasts", "fungi")))),
|
||||
c("F_YEAST", "F_FUNGUS")
|
||||
)
|
||||
# assigning and subsetting
|
||||
x <- example_isolates$mo
|
||||
expect_inherits(x[1], "mo")
|
||||
expect_inherits(x[[1]], "mo")
|
||||
expect_inherits(c(x[1], x[9]), "mo")
|
||||
# expect_warning(x[1] <- "invalid code")
|
||||
# expect_warning(x[[1]] <- "invalid code")
|
||||
# expect_warning(c(x[1], "test"))
|
||||
|
||||
if (AMR:::pkg_is_available("tibble")) {
|
||||
# print tibble
|
||||
expect_stdout(print(tibble::tibble(mo = as.mo("B_ESCHR_COLI"))))
|
||||
}
|
||||
# ignoring patterns
|
||||
expect_true(is.na(as.mo("E. coli ignorethis", ignore_pattern = "this")))
|
||||
|
||||
# assigning and subsetting
|
||||
x <- example_isolates$mo
|
||||
expect_inherits(x[1], "mo")
|
||||
expect_inherits(x[[1]], "mo")
|
||||
expect_inherits(c(x[1], x[9]), "mo")
|
||||
# expect_warning(x[1] <- "invalid code")
|
||||
# expect_warning(x[[1]] <- "invalid code")
|
||||
# expect_warning(c(x[1], "test"))
|
||||
|
||||
# ignoring patterns
|
||||
expect_true(is.na(as.mo("E. coli ignorethis", ignore_pattern = "this")))
|
||||
|
||||
# frequency tables
|
||||
if (AMR:::pkg_is_available("cleaner")) {
|
||||
expect_inherits(cleaner::freq(example_isolates$mo), "freq")
|
||||
}
|
||||
# frequency tables
|
||||
if (AMR:::pkg_is_available("cleaner")) {
|
||||
expect_inherits(cleaner::freq(example_isolates$mo), "freq")
|
||||
}
|
||||
})
|
||||
|
||||
Reference in New Issue
Block a user