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AMR/inst/tinytest/test-mo_property.R

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# ==================================================================== #
# TITLE: #
# AMR: An R Package for Working with Antimicrobial Resistance Data #
# #
# SOURCE CODE: #
# https://github.com/msberends/AMR #
# #
# PLEASE CITE THIS SOFTWARE AS: #
# Berends MS, Luz CF, Friedrich AW, et al. (2022). #
# AMR: An R Package for Working with Antimicrobial Resistance Data. #
# Journal of Statistical Software, 104(3), 1-31. #
# https://doi.org/10.18637/jss.v104.i03 #
# #
# Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many #
# colleagues from around the world, see our website. #
# #
# 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. #
# We created this package for both routine data analysis and academic #
# research and it was publicly released in the hope that it will be #
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# ==================================================================== #
expect_equal(mo_kingdom("Escherichia coli"), "Bacteria")
expect_equal(mo_kingdom("Escherichia coli"), mo_domain("Escherichia coli"))
expect_equal(mo_phylum("Escherichia coli"), "Pseudomonadota")
expect_equal(mo_class("Escherichia coli"), "Gammaproteobacteria")
expect_equal(mo_order("Escherichia coli"), "Enterobacterales")
expect_equal(mo_family("Escherichia coli"), "Enterobacteriaceae")
expect_equal(mo_fullname("Escherichia coli"), "Escherichia coli")
expect_equal(mo_genus("Escherichia coli"), "Escherichia")
expect_equal(mo_name("Escherichia coli"), "Escherichia coli")
expect_equal(mo_shortname("Escherichia coli"), "E. coli")
expect_equal(mo_shortname("Escherichia"), "Escherichia")
expect_equal(mo_shortname("Staphylococcus aureus"), "S. aureus")
expect_equal(mo_shortname("Staphylococcus aureus", Becker = TRUE), "S. aureus")
expect_equal(mo_shortname("Staphylococcus aureus", Becker = "all", language = "en"), "CoPS")
expect_equal(mo_shortname("Streptococcus agalactiae"), "S. agalactiae")
expect_equal(mo_shortname("Streptococcus agalactiae", Lancefield = TRUE), "GBS")
# check gram stain determination, to prevent we lag after a taxonomic renaming
current_grampos_phyla <- c(
"Actinomycetota", # since 2021, old name was Actinobacteria
"Chloroflexota", # since 2021, old name was Chloroflexi
"Bacillota", # since 2021, old name was Firmicutes
"Mycoplasmatota" # since 2021, old name was Tenericutes
)
expect_true(all(current_grampos_phyla %in% microorganisms$phylum, na.rm = TRUE))
current_grampos_classes <- c(
"",
"Acidimicrobiia",
"Actinomycetes",
"Anaerolineae",
"Ardenticatenia",
"Bacilli",
"Caldilineae",
"Chloroflexia",
"Clostridia",
"Coriobacteriia",
"Culicoidibacteria",
"Dehalococcoidia",
"Erysipelotrichia",
"Ktedonobacteria",
"Limnochordia",
"Limnocylindria",
"Mollicutes",
"Negativicutes",
"Nitriliruptoria",
"Rubrobacteria",
"Tepidiformia",
"Thermoflexia",
"Thermoleophilia",
"Thermolithobacteria"
)
expect_identical(sort(unique(microorganisms[which(microorganisms$phylum %in% current_grampos_phyla), "class", drop = TRUE])),
current_grampos_classes)
expect_equal(mo_species("Escherichia coli"), "coli")
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(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(
"mo", "rank",
"kingdom", "phylum", "class", "order", "family", "genus", "species", "subspecies",
"status", "synonyms", "gramstain", "oxygen_tolerance",
"url", "ref", "snomed", "lpsn", "mycobank", "gbif", "group_members"
))
expect_inherits(mo_info(c("Escherichia coli", "Staphylococcus aureus")), "list")
expect_true(length(mo_group_members("B_HACEK")) > 1)
expect_inherits(mo_group_members(c("Candida albicans", "Escherichia coli")), "list")
expect_identical(mo_oxygen_tolerance(c("Klebsiella pneumoniae", "Clostridioides difficile")),
c("facultative anaerobe", "anaerobe"))
expect_equal(as.character(table(mo_pathogenicity(example_isolates$mo))),
c("1911", "72", "1", "16"))
expect_equal(mo_ref("Escherichia coli"), "Castellani et al., 1919")
expect_equal(mo_authors("Escherichia coli"), "Castellani et al.")
expect_equal(mo_year("Escherichia coli"), 1919)
expect_true(mo_url("Amoeba dysenteriae") %like% "gbif.org")
expect_true(mo_url("Candida albicans") %like% "mycobank.org")
expect_true(mo_url("Escherichia coli") %like% "lpsn.dsmz.de")
# test integrity of getting back full names
expect_identical(microorganisms$fullname[microorganisms$fullname %unlike% "(Fungi|{)"],
suppressWarnings(mo_fullname(microorganisms$fullname[microorganisms$fullname %unlike% "(Fungi|{)"], language = "en", keep_synonyms = TRUE)))
# check languages
expect_equal(mo_type("Escherichia coli", language = "de"), "Bakterien")
expect_equal(mo_gramstain("Escherichia coli", language = "nl"), "Gram-negatief")
gr <- mo_gramstain("Escherichia coli", language = NULL)
for (l in AMR:::LANGUAGES_SUPPORTED[-1]) {
expect_false(mo_gramstain("Escherichia coli", language = l) == gr, info = paste("Gram-stain in language", l))
}
# test languages
expect_error(mo_gramstain("Escherichia coli", language = "UNKNOWN"))
fullnames <- microorganisms$fullname[which(microorganisms$fullname %unlike% "unknown|coagulase|Fungi|[(]class[)]|[{]")]
to_dutch <- suppressWarnings(mo_name(fullnames, language = "nl", keep_synonyms = TRUE))
back_to_english <- suppressWarnings(mo_name(to_dutch, language = NULL, keep_synonyms = TRUE))
diffs <- paste0('"', fullnames[fullnames != back_to_english], '"', collapse = ", ")
expect_identical(fullnames, back_to_english, info = diffs) # gigantic test - will run ALL names
# manual property function
expect_error(mo_property("Escherichia coli", property = c("genus", "fullname")))
expect_error(mo_property("Escherichia coli", property = "UNKNOWN"))
expect_identical(
mo_property("Escherichia coli", property = "fullname"),
mo_fullname("Escherichia coli")
)
expect_identical(
mo_property("Escherichia coli", property = "genus"),
mo_genus("Escherichia coli")
)
expect_identical(
mo_property("Escherichia coli", property = "species"),
mo_species("Escherichia coli")
)
expect_identical(
mo_property("Escherichia coli", property = "lpsn"),
mo_lpsn("Escherichia coli")
)
expect_identical(
mo_property("Escherichia coli", property = "gbif"),
mo_gbif("Escherichia coli")
)
expect_identical(
mo_property("Absidia abundans", property = "mycobank"),
mo_mycobank("Absidia abundans")
)
expect_true("Escherichia blattae" %in% mo_synonyms("Shimwellia blattae"))
expect_true(is.list(mo_synonyms(rep("Shimwellia blattae", 2))))
expect_identical(mo_current(c("Escherichia blattae", "Escherichia coli")),
c("Shimwellia blattae", "Escherichia coli"))
expect_identical(mo_ref("Chlamydia psittaci"), "Garcia-Lopez et al., 2019")
expect_identical(mo_ref("Chlamydophila psittaci", keep_synonyms = TRUE), "Everett et al., 1999")
expect_true(112283007 %in% mo_snomed("Escherichia coli")[[1]])
# outcome of mo_fullname must always return the fullname from the data set
x <- data.frame(
mo = microorganisms$mo,
# fullname from the original data:
f1 = microorganisms$fullname,
# newly created fullname based on MO code:
f2 = mo_fullname(microorganisms$mo, language = "en", keep_synonyms = TRUE),
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_yeast(c("Candida", "Trichophyton", "Klebsiella")),
c(TRUE, FALSE, FALSE)
)
# is intrinsic resistant
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"
)
if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0", also_load = TRUE)) {
expect_equal(example_isolates %>% filter(mo_is_gram_negative()) %>% nrow(),
730,
tolerance = 0.5
)
expect_equal(example_isolates %>% filter(mo_is_gram_positive()) %>% nrow(),
1238,
tolerance = 0.5
)
expect_equal(example_isolates %>% filter(mo_is_intrinsic_resistant(ab = "Vancomycin")) %>% nrow(),
710,
tolerance = 0.5
)
}
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