mirror of https://github.com/msberends/AMR.git
215 lines
9.2 KiB
R
215 lines
9.2 KiB
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(
|
|
"mo",
|
|
"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$fullname %unlike% "unknown|coagulase|Fungi|[(]class[)]|[{]")]) # gigantic test - will run ALL names
|
|
|
|
# manual property function
|
|
expect_error(mo_property("Escherichia coli", property = c("genus", "fullname")))
|
|
expect_error(mo_property("Escherichia coli", property = "UNKNOWN"))
|
|
expect_identical(
|
|
mo_property("Escherichia coli", property = "fullname"),
|
|
mo_fullname("Escherichia coli")
|
|
)
|
|
expect_identical(
|
|
mo_property("Escherichia coli", property = "genus"),
|
|
mo_genus("Escherichia coli")
|
|
)
|
|
expect_identical(
|
|
mo_property("Escherichia coli", property = "species"),
|
|
mo_species("Escherichia coli")
|
|
)
|
|
expect_identical(
|
|
mo_property("Escherichia coli", property = "lpsn"),
|
|
mo_lpsn("Escherichia coli")
|
|
)
|
|
expect_identical(
|
|
mo_property("Escherichia coli", property = "gbif"),
|
|
mo_gbif("Escherichia coli")
|
|
)
|
|
|
|
expect_true("Escherichia blattae" %in% mo_synonyms("Shimwellia blattae"))
|
|
expect_true(is.list(mo_synonyms(rep("Shimwellia blattae", 2))))
|
|
expect_identical(mo_current(c("Escherichia blattae", "Escherichia coli")),
|
|
c("Shimwellia blattae", "Escherichia coli"))
|
|
|
|
expect_identical(mo_ref("Chlamydia psittaci"), "Garcia-Lopez et al., 2019")
|
|
expect_identical(mo_ref("Chlamydophila psittaci", keep_synonyms = TRUE), "Everett et al., 1999")
|
|
|
|
expect_true(112283007 %in% mo_snomed("Escherichia coli")[[1]])
|
|
# old codes must throw a warning in mo_* family
|
|
# expect_warning(mo_name(c("B_ESCHR_COL", "B_STPHY_AUR")))
|
|
# outcome of mo_fullname must always return the fullname from the data set
|
|
x <- data.frame(
|
|
mo = microorganisms$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", 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
|
|
)
|
|
}
|