mirror of https://github.com/msberends/AMR.git
220 lines
9.5 KiB
R
220 lines
9.5 KiB
R
# ==================================================================== #
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# TITLE: #
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# AMR: An R Package for Working with Antimicrobial Resistance Data #
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# #
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# SOURCE CODE: #
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# https://github.com/msberends/AMR #
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# #
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# PLEASE CITE THIS SOFTWARE AS: #
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# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
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# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
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# Data. Journal of Statistical Software, 104(3), 1-31. #
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# https://doi.org/10.18637/jss.v104.i03 #
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# #
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# Developed at the University of Groningen and the University Medical #
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# Center Groningen in The Netherlands, in collaboration with many #
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# colleagues from around the world, see our website. #
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# #
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# This R package is free software; you can freely use and distribute #
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# it for both personal and commercial purposes under the terms of the #
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# GNU General Public License version 2.0 (GNU GPL-2), as published by #
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# the Free Software Foundation. #
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# We created this package for both routine data analysis and academic #
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# research and it was publicly released in the hope that it will be #
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# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
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# #
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# Visit our website for the full manual and a complete tutorial about #
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# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
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# ==================================================================== #
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expect_equal(mo_kingdom("Escherichia coli"), "Bacteria")
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expect_equal(mo_kingdom("Escherichia coli"), mo_domain("Escherichia coli"))
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expect_equal(mo_phylum("Escherichia coli"), "Pseudomonadota")
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expect_equal(mo_class("Escherichia coli"), "Gammaproteobacteria")
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expect_equal(mo_order("Escherichia coli"), "Enterobacterales")
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expect_equal(mo_family("Escherichia coli"), "Enterobacteriaceae")
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expect_equal(mo_fullname("Escherichia coli"), "Escherichia coli")
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expect_equal(mo_genus("Escherichia coli"), "Escherichia")
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expect_equal(mo_name("Escherichia coli"), "Escherichia coli")
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expect_equal(mo_shortname("Escherichia coli"), "E. coli")
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expect_equal(mo_shortname("Escherichia"), "Escherichia")
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expect_equal(mo_shortname("Staphylococcus aureus"), "S. aureus")
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expect_equal(mo_shortname("Staphylococcus aureus", Becker = TRUE), "S. aureus")
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expect_equal(mo_shortname("Staphylococcus aureus", Becker = "all", language = "en"), "CoPS")
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expect_equal(mo_shortname("Streptococcus agalactiae"), "S. agalactiae")
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expect_equal(mo_shortname("Streptococcus agalactiae", Lancefield = TRUE), "GBS")
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# check gram stain determination, to prevent we lag after a taxonomic renaming
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current_grampos_phyla <- c(
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"Actinomycetota", # since 2021, old name was Actinobacteria
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"Chloroflexota", # since 2021, old name was Chloroflexi
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"Bacillota", # since 2021, old name was Firmicutes
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"Mycoplasmatota" # since 2021, old name was Tenericutes
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)
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expect_true(all(current_grampos_phyla %in% microorganisms$phylum, na.rm = TRUE))
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current_grampos_classes <- c(
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"",
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"Acidimicrobiia",
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"Actinomycetes",
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"Anaerolineae",
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"Ardenticatenia",
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"Bacilli",
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"Caldilineae",
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"Chloroflexia",
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"Clostridia",
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"Coriobacteriia",
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"Culicoidibacteria",
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"Dehalococcoidia",
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"Erysipelotrichia",
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"Ktedonobacteria",
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"Limnochordia",
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"Limnocylindria",
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"Mollicutes",
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"Negativicutes",
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"Nitriliruptoria",
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"Rubrobacteria",
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"Tepidiformia",
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"Thermoflexia",
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"Thermoleophilia",
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"Thermolithobacteria",
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"Tissierellia"
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)
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expect_identical(sort(unique(microorganisms[which(microorganisms$phylum %in% current_grampos_phyla), "class", drop = TRUE])),
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current_grampos_classes)
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expect_equal(mo_species("Escherichia coli"), "coli")
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expect_equal(mo_subspecies("Escherichia coli"), "")
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expect_equal(mo_type("Escherichia coli", language = "en"), "Bacteria")
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expect_equal(mo_gramstain("Escherichia coli", language = "en"), "Gram-negative")
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expect_inherits(mo_taxonomy("Escherichia coli"), "list")
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expect_equal(names(mo_taxonomy("Escherichia coli")), c(
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"kingdom", "phylum", "class", "order",
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"family", "genus", "species", "subspecies"
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))
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expect_equal(mo_synonyms("Escherichia coli"), NULL)
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expect_true(length(mo_synonyms("Candida albicans")) > 1)
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expect_inherits(mo_synonyms(c("Candida albicans", "Escherichia coli")), "list")
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expect_equal(names(mo_info("Escherichia coli")), c(
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"mo",
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"kingdom", "phylum", "class", "order", "family", "genus", "species", "subspecies",
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"status", "synonyms", "gramstain", "oxygen_tolerance",
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"url", "ref", "snomed", "lpsn", "gbif", "group_members"
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))
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expect_inherits(mo_info(c("Escherichia coli", "Staphylococcus aureus")), "list")
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expect_true(length(mo_group_members("B_HACEK")) > 1)
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expect_inherits(mo_group_members(c("Candida albicans", "Escherichia coli")), "list")
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expect_identical(mo_oxygen_tolerance(c("Klebsiella pneumoniae", "Clostridioides difficile")),
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c("aerobe", "anaerobe"))
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expect_equal(as.character(table(mo_pathogenicity(example_isolates$mo))),
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c("1874", "109", "1", "16"))
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expect_equal(mo_ref("Escherichia coli"), "Castellani et al., 1919")
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expect_equal(mo_authors("Escherichia coli"), "Castellani et al.")
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expect_equal(mo_year("Escherichia coli"), 1919)
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expect_true(mo_url("Candida albicans") %like% "gbif.org")
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expect_true(mo_url("Escherichia coli") %like% "lpsn.dsmz.de")
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# test integrity
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expect_identical(microorganisms$fullname, mo_fullname(microorganisms$fullname, language = "en", keep_synonyms = TRUE))
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# check languages
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expect_equal(mo_type("Escherichia coli", language = "de"), "Bakterien")
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expect_equal(mo_gramstain("Escherichia coli", language = "nl"), "Gram-negatief")
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gr <- mo_gramstain("Escherichia coli", language = NULL)
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for (l in AMR:::LANGUAGES_SUPPORTED[-1]) {
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expect_false(mo_gramstain("Escherichia coli", language = l) == gr, info = paste("Gram-stain in language", l))
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}
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# test languages
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expect_error(mo_gramstain("Escherichia coli", language = "UNKNOWN"))
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fullnames <- microorganisms$fullname[which(microorganisms$fullname %unlike% "unknown|coagulase|Fungi|[(]class[)]|[{]")]
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to_dutch <- suppressWarnings(mo_name(fullnames, language = "nl", keep_synonyms = TRUE))
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back_to_english <- suppressWarnings(mo_name(to_dutch, language = NULL, keep_synonyms = TRUE))
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diffs <- paste0('"', fullnames[fullnames != back_to_english], '"', collapse = ", ")
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expect_identical(fullnames, back_to_english, info = diffs) # gigantic test - will run ALL names
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# manual property function
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expect_error(mo_property("Escherichia coli", property = c("genus", "fullname")))
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expect_error(mo_property("Escherichia coli", property = "UNKNOWN"))
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expect_identical(
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mo_property("Escherichia coli", property = "fullname"),
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mo_fullname("Escherichia coli")
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)
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expect_identical(
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mo_property("Escherichia coli", property = "genus"),
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mo_genus("Escherichia coli")
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)
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expect_identical(
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mo_property("Escherichia coli", property = "species"),
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mo_species("Escherichia coli")
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)
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expect_identical(
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mo_property("Escherichia coli", property = "lpsn"),
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mo_lpsn("Escherichia coli")
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)
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expect_identical(
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mo_property("Escherichia coli", property = "gbif"),
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mo_gbif("Escherichia coli")
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)
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expect_true("Escherichia blattae" %in% mo_synonyms("Shimwellia blattae"))
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expect_true(is.list(mo_synonyms(rep("Shimwellia blattae", 2))))
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expect_identical(mo_current(c("Escherichia blattae", "Escherichia coli")),
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c("Shimwellia blattae", "Escherichia coli"))
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expect_identical(mo_ref("Chlamydia psittaci"), "Garcia-Lopez et al., 2019")
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expect_identical(mo_ref("Chlamydophila psittaci", keep_synonyms = TRUE), "Everett et al., 1999")
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expect_true(112283007 %in% mo_snomed("Escherichia coli")[[1]])
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# outcome of mo_fullname must always return the fullname from the data set
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x <- data.frame(
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mo = microorganisms$mo,
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# fullname from the original data:
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f1 = microorganisms$fullname,
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# newly created fullname based on MO code:
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f2 = mo_fullname(microorganisms$mo, language = "en", keep_synonyms = TRUE),
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stringsAsFactors = FALSE
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)
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expect_equal(nrow(subset(x, f1 != f2)), 0)
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# is gram pos/neg (also return FALSE for all non-bacteria)
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expect_equal(
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mo_is_gram_negative(c("Escherichia coli", "Staphylococcus aureus", "Candida albicans")),
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c(TRUE, FALSE, FALSE)
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)
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expect_equal(
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mo_is_gram_positive(c("Escherichia coli", "Staphylococcus aureus", "Candida albicans")),
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c(FALSE, TRUE, FALSE)
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)
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# is intrinsic resistant
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expect_equal(
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mo_is_intrinsic_resistant(
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c("Escherichia coli", "Staphylococcus aureus", "Candida albicans"),
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"vanco"
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),
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c(TRUE, FALSE, FALSE)
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)
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# with reference data
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expect_equal(
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mo_name("test", reference_df = data.frame(col1 = "test", mo = "B_ESCHR_COLI")),
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"Escherichia coli"
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)
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if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0", also_load = TRUE)) {
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expect_equal(example_isolates %>% filter(mo_is_gram_negative()) %>% nrow(),
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730,
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tolerance = 0.5
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)
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expect_equal(example_isolates %>% filter(mo_is_gram_positive()) %>% nrow(),
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1238,
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tolerance = 0.5
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)
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expect_equal(example_isolates %>% filter(mo_is_intrinsic_resistant(ab = "Vancomycin")) %>% nrow(),
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710,
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tolerance = 0.5
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)
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}
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