mirror of https://github.com/msberends/AMR.git
124 lines
5.2 KiB
R
124 lines
5.2 KiB
R
context("bactid.R")
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test_that("as.bactid works", {
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expect_identical(
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as.character(as.bactid(c("E. coli", "H. influenzae"))),
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c("ESCCOL", "HAEINF"))
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expect_equal(as.character(as.bactid("Escherichia coli")), "ESCCOL")
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expect_equal(as.character(as.bactid("Escherichia coli")), "ESCCOL")
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expect_equal(as.character(as.bactid("Escherichia species")), "ESC")
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expect_equal(as.character(as.bactid(" ESCCOL ")), "ESCCOL")
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expect_equal(as.character(as.bactid("klpn")), "KLEPNE")
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expect_equal(as.character(as.bactid("P. aer")), "PSEAER") # not Pasteurella aerogenes
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expect_equal(as.character(as.bactid("Negative rods")), "GNR")
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# GLIMS
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expect_equal(as.character(as.bactid("shiboy")), "SHIBOY")
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expect_equal(as.character(as.bactid("MRSE")), "STAEPI")
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expect_equal(as.character(as.bactid("VRE")), "ENC")
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expect_equal(as.character(as.bactid("MRPA")), "PSEAER")
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expect_equal(as.character(as.bactid("PISP")), "STCPNE")
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expect_equal(as.character(as.bactid("PRSP")), "STCPNE")
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expect_equal(as.character(as.bactid("VISP")), "STCPNE")
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expect_equal(as.character(as.bactid("VRSP")), "STCPNE")
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expect_identical(
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as.character(
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as.bactid(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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"Staphylococcus aureus",
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"MRSA",
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"VISA"))),
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rep("STAAUR", 8))
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# check for Becker classification
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expect_identical(as.character(guess_bactid("S. epidermidis", Becker = FALSE)), "STAEPI")
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expect_identical(as.character(guess_bactid("S. epidermidis", Becker = TRUE)), "STACNS")
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expect_identical(as.character(guess_bactid("STAEPI", Becker = TRUE)), "STACNS")
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expect_identical(as.character(guess_bactid("S. intermedius", Becker = FALSE)), "STAINT")
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expect_identical(as.character(guess_bactid("S. intermedius", Becker = TRUE)), "STACPS")
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expect_identical(as.character(guess_bactid("STAINT", Becker = TRUE)), "STACPS")
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# aureus must only be influenced if Becker = "all"
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expect_identical(as.character(guess_bactid("STAAUR", Becker = FALSE)), "STAAUR")
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expect_identical(as.character(guess_bactid("STAAUR", Becker = TRUE)), "STAAUR")
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expect_identical(as.character(guess_bactid("STAAUR", Becker = "all")), "STACPS")
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# check for Lancefield classification
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expect_identical(as.character(guess_bactid("S. pyogenes", Lancefield = FALSE)), "STCPYO")
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expect_identical(as.character(guess_bactid("S. pyogenes", Lancefield = TRUE)), "STCGRA")
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expect_identical(as.character(guess_bactid("STCPYO", Lancefield = TRUE)), "STCGRA")
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expect_identical(as.character(guess_bactid("S. agalactiae", Lancefield = FALSE)), "STCAGA")
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expect_identical(as.character(guess_bactid("S. agalactiae", Lancefield = TRUE)), "STCGRB") # group B
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expect_identical(as.character(guess_bactid("S. equisimilis", Lancefield = FALSE)), "STCEQS")
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expect_identical(as.character(guess_bactid("S. equisimilis", Lancefield = TRUE)), "STCGRC") # group C
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expect_identical(as.character(guess_bactid("S. anginosus", Lancefield = FALSE)), "STCANG")
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expect_identical(as.character(guess_bactid("S. anginosus", Lancefield = TRUE)), "STCGRF") # group F
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expect_identical(as.character(guess_bactid("S. sanguis", Lancefield = FALSE)), "STCSAN")
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expect_identical(as.character(guess_bactid("S. sanguis", Lancefield = TRUE)), "STCGRH") # group H
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expect_identical(as.character(guess_bactid("S. salivarius", Lancefield = FALSE)), "STCSAL")
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expect_identical(as.character(guess_bactid("S. salivarius", Lancefield = TRUE)), "STCGRK") # group K
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# select with one column
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expect_identical(
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septic_patients[1:10,] %>%
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left_join_microorganisms() %>%
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select(genus) %>%
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as.bactid() %>%
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as.character(),
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c("ESC", "ESC", "STA", "STA", "STA",
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"STA", "STA", "STA", "STA", "STA"))
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# select with two columns
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expect_identical(
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septic_patients[1:10,] %>%
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pull(bactid),
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septic_patients[1:10,] %>%
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left_join_microorganisms() %>%
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select(genus, species) %>%
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as.bactid() %>%
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as.character())
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# unknown results
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expect_warning(as.bactid(c("INVALID", "Yeah, unknown")))
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# print
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expect_output(print(as.bactid(c("ESCCOL", NA))))
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# helper function
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expect_identical(as.bactid("ESCCOL"),
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guess_bactid("ESCCOL"))
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# test pull
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expect_equal(nrow(septic_patients %>% mutate(bactid = as.bactid(bactid))),
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2000)
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# test data.frame
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expect_equal(nrow(data.frame(test = as.bactid("ESCCOL"))),
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1)
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# check empty values
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expect_equal(as.character(suppressWarnings(as.bactid(""))),
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NA_character_)
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})
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test_that("bactid.property works", {
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expect_equal(bactid.family("E. coli"), "Enterobacteriaceae")
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expect_equal(bactid.genus("E. coli"), "Escherichia")
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expect_equal(bactid.species("E. coli"), "coli")
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expect_equal(bactid.subspecies("E. coli"), NA_character_)
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expect_equal(bactid.fullname("E. coli"), "Escherichia coli")
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expect_equal(bactid.type("E. coli"), "Bacteria")
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expect_equal(bactid.gramstain("E. coli"), "Negative rods")
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expect_equal(bactid.aerobic("E. coli"), TRUE)
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expect_equal(bactid.type_nl("E. coli"), "Bacterie")
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expect_equal(bactid.gramstain_nl("E. coli"), "Negatieve staven")
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})
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