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styled, unit test fix

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dr. M.S. (Matthijs) Berends
2022-08-28 10:31:50 +02:00
parent 4cb1db4554
commit 4d050aef7c
147 changed files with 10897 additions and 8169 deletions
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96
inst/tinytest/test-mo_property.R
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@ -9,7 +9,7 @@
# (c) 2018-2022 Berends MS, Luz CF et al. #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #
# Diagnostics & Advice, and University Medical Center Groningen. #
# #
# This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the #
@ -45,15 +45,19 @@ expect_equal(mo_subspecies("Escherichia coli"), "")
expect_equal(mo_type("Escherichia coli", language = "en"), "Bacteria")
expect_equal(mo_gramstain("Escherichia coli", language = "en"), "Gram-negative")
expect_inherits(mo_taxonomy("Escherichia coli"), "list")
expect_equal(names(mo_taxonomy("Escherichia coli")), c("kingdom", "phylum", "class", "order",
"family", "genus", "species", "subspecies"))
expect_equal(names(mo_taxonomy("Escherichia coli")), c(
"kingdom", "phylum", "class", "order",
"family", "genus", "species", "subspecies"
))
expect_equal(mo_synonyms("Escherichia coli"), NULL)
expect_true(length(mo_synonyms("Candida albicans")) > 1)
expect_inherits(mo_synonyms(c("Candida albicans", "Escherichia coli")), "list")
expect_equal(names(mo_info("Escherichia coli")), c("kingdom", "phylum", "class", "order",
"family", "genus", "species", "subspecies",
"synonyms", "gramstain", "url", "ref",
"snomed"))
expect_equal(names(mo_info("Escherichia coli")), c(
"kingdom", "phylum", "class", "order",
"family", "genus", "species", "subspecies",
"synonyms", "gramstain", "url", "ref",
"snomed"
))
expect_inherits(mo_info(c("Escherichia coli", "Staphylococcus aureus")), "list")
expect_equal(mo_ref("Escherichia coli"), "Castellani et al., 1919")
@ -86,14 +90,22 @@ expect_identical(mo_name(dutch, language = NULL), microorganisms$fullname) # gig
# manual property function
expect_error(mo_property("Escherichia coli", property = c("tsn", "fullname")))
expect_error(mo_property("Escherichia coli", property = "UNKNOWN"))
expect_identical(mo_property("Escherichia coli", property = "fullname"),
mo_fullname("Escherichia coli"))
expect_identical(mo_property("Escherichia coli", property = "genus"),
mo_genus("Escherichia coli"))
expect_identical(mo_property("Escherichia coli", property = "species"),
mo_species("Escherichia coli"))
expect_identical(mo_property("Escherichia coli", property = "species_id"),
mo_lpsn("Escherichia coli"))
expect_identical(
mo_property("Escherichia coli", property = "fullname"),
mo_fullname("Escherichia coli")
)
expect_identical(
mo_property("Escherichia coli", property = "genus"),
mo_genus("Escherichia coli")
)
expect_identical(
mo_property("Escherichia coli", property = "species"),
mo_species("Escherichia coli")
)
expect_identical(
mo_property("Escherichia coli", property = "species_id"),
mo_lpsn("Escherichia coli")
)
expect_identical(suppressWarnings(mo_ref("Chlamydia psittaci")), "Page, 1968")
expect_identical(mo_ref("Chlamydophila psittaci"), "Everett et al., 1999")
@ -102,30 +114,48 @@ expect_true(112283007 %in% mo_snomed("Escherichia coli"))
# old codes must throw a warning in mo_* family
expect_warning(mo_name(c("B_ESCHR_COL", "B_STPHY_AUR")))
# outcome of mo_fullname must always return the fullname from the data set
x <- data.frame(mo = microorganisms$mo,
# fullname from the original data:
f1 = microorganisms$fullname,
# newly created fullname based on MO code:
f2 = mo_fullname(microorganisms$mo, language = "en"),
stringsAsFactors = FALSE)
x <- data.frame(
mo = microorganisms$mo,
# fullname from the original data:
f1 = microorganisms$fullname,
# newly created fullname based on MO code:
f2 = mo_fullname(microorganisms$mo, language = "en"),
stringsAsFactors = FALSE
)
expect_equal(nrow(subset(x, f1 != f2)), 0)
# is gram pos/neg (also return FALSE for all non-bacteria)
expect_equal(mo_is_gram_negative(c("Escherichia coli", "Staphylococcus aureus", "Candida albicans")),
c(TRUE, FALSE, FALSE))
expect_equal(mo_is_gram_positive(c("Escherichia coli", "Staphylococcus aureus", "Candida albicans")),
c(FALSE, TRUE, FALSE))
expect_equal(
mo_is_gram_negative(c("Escherichia coli", "Staphylococcus aureus", "Candida albicans")),
c(TRUE, FALSE, FALSE)
)
expect_equal(
mo_is_gram_positive(c("Escherichia coli", "Staphylococcus aureus", "Candida albicans")),
c(FALSE, TRUE, FALSE)
)
# is intrinsic resistant
expect_equal(mo_is_intrinsic_resistant(c("Escherichia coli", "Staphylococcus aureus", "Candida albicans"),
"vanco"),
c(TRUE, FALSE, FALSE))
expect_equal(
mo_is_intrinsic_resistant(
c("Escherichia coli", "Staphylococcus aureus", "Candida albicans"),
"vanco"
),
c(TRUE, FALSE, FALSE)
)
# with reference data
expect_equal(mo_name("test", reference_df = data.frame(col1 = "test", mo = "B_ESCHR_COLI")),
"Escherichia coli")
expect_equal(
mo_name("test", reference_df = data.frame(col1 = "test", mo = "B_ESCHR_COLI")),
"Escherichia coli"
)
if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
expect_equal(example_isolates %>% filter(mo_is_gram_negative()) %>% nrow(),
730, tolerance = 0.5)
730,
tolerance = 0.5
)
expect_equal(example_isolates %>% filter(mo_is_gram_positive()) %>% nrow(),
1238, tolerance = 0.5)
1238,
tolerance = 0.5
)
expect_equal(example_isolates %>% filter(mo_is_intrinsic_resistant(ab = "Vancomycin")) %>% nrow(),
710, tolerance = 0.5)
710,
tolerance = 0.5
)
}