AMR/inst/tinytest/test-mo_property.R

# ==================================================================== #
# TITLE                                                                #
# AMR: An R Package for Working with Antimicrobial Resistance Data     #
#                                                                      #
# SOURCE                                                               #
# https://github.com/msberends/AMR                                     #
#                                                                      #
# CITE AS                                                              #
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C    #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance  #
# Data. Journal of Statistical Software, 104(3), 1-31.                 #
# doi: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$phylum, na.rm = TRUE))
current_grampos_classes <- c(
  "",
  "Acidimicrobiia",
  "Actinomycetes",
  "Anaerolineae",
  "Ardenticatenia",
  "Bacilli",
  "Caldilineae",
  "Chloroflexia",
  "Clostridia",
  "Coriobacteriia",
  "Culicoidibacteria",
  "Dehalococcoidia",
  "Erysipelotrichia",
  "Ktedonobacteria",
  "Limnochordia",
  "Limnocylindria",
  "Mollicutes",
  "Negativicutes",
  "Nitriliruptoria",
  "Rubrobacteria",
  "Tepidiformia",
  "Thermoflexia",
  "Thermoleophilia",
  "Thermolithobacteria",
  "Tissierellia"
)
expect_identical(sort(unique(microorganisms[which(microorganisms$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(
  "identifier",
  "kingdom", "phylum", "class", "order",
  "family", "genus", "species", "subspecies",
  "status", "synonyms", "gramstain", "url", "ref",
  "snomed"
))
expect_inherits(mo_info(c("Escherichia coli", "Staphylococcus aureus")), "list")

expect_equal(as.character(table(mo_pathogenicity(example_isolates$mo))),
             c("1561", "422", "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("Candida albicans") %like% "gbif.org")
expect_true(mo_url("Escherichia coli") %like% "lpsn.dsmz.de")

# test integrity
expect_identical(microorganisms$fullname, mo_fullname(microorganisms$fullname, 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"))
dutch <- suppressWarnings(mo_name(microorganisms$fullname[which(microorganisms$fullname %unlike% "unknown|coagulase|Fungi|[(]class[)]|[{]")], language = "nl", keep_synonyms = TRUE)) # should be transformable to English again
expect_identical(suppressWarnings(mo_name(dutch, language = NULL, keep_synonyms = TRUE)),
                 microorganisms$fullname[which(microorganisms$fullname %unlike% "unknown|coagulase|Fungi|[(]class[)]|[{]")]) # 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_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"))
# 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
)
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)
)
# 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")) {
  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
  )
}