# ==================================================================== # # TITLE # # Antimicrobial Resistance (AMR) Data Analysis for R # # # # SOURCE # # https://github.com/msberends/AMR # # # # LICENCE # # (c) 2018-2021 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. # # # # 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/ # # ==================================================================== # context("mo_property.R") test_that("mo_property works", { skip_on_cran() expect_equal(mo_kingdom("Escherichia coli"), "Bacteria") expect_equal(mo_kingdom("Escherichia coli"), mo_domain("Escherichia coli")) expect_equal(mo_phylum("Escherichia coli"), "Proteobacteria") expect_equal(mo_class("Escherichia coli"), "Gammaproteobacteria") expect_equal(mo_order("Escherichia coli"), "Enterobacterales") expect_equal(mo_family("Escherichia coli"), "Enterobacteriaceae") expect_equal(mo_genus("Escherichia coli"), "Escherichia") expect_equal(mo_species("Escherichia coli"), "coli") expect_equal(mo_subspecies("Escherichia coli"), "") expect_equal(mo_fullname("Escherichia coli"), "Escherichia coli") expect_equal(mo_name("Escherichia coli"), "Escherichia coli") expect_equal(mo_type("Escherichia coli", language = "en"), "Bacteria") expect_equal(mo_gramstain("Escherichia coli", language = "en"), "Gram-negative") expect_equal(class(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_gt(length(mo_synonyms("Candida albicans")), 1) expect_equal(class(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(class(mo_info(c("Escherichia coli", "Staphylococcus aureus"))), "list") 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_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") expect_true(mo_url("Candida albicans") %like% "catalogueoflife.org") expect_true(mo_url("Escherichia coli") %like% "lpsn.dsmz.de") # test integrity MOs <- microorganisms expect_identical(MOs$fullname, mo_fullname(MOs$fullname, language = "en")) # check languages expect_equal(mo_type("Escherichia coli", language = "de"), "Bakterien") expect_equal(mo_gramstain("Escherichia coli", language = "nl"), "Gram-negatief") expect_output(print(mo_gramstain("Escherichia coli", language = "en"))) expect_output(print(mo_gramstain("Escherichia coli", language = "de"))) expect_output(print(mo_gramstain("Escherichia coli", language = "nl"))) expect_output(print(mo_gramstain("Escherichia coli", language = "es"))) expect_output(print(mo_gramstain("Escherichia coli", language = "pt"))) expect_output(print(mo_gramstain("Escherichia coli", language = "it"))) expect_output(print(mo_gramstain("Escherichia coli", language = "fr"))) expect_error(mo_gramstain("Escherichia coli", language = "UNKNOWN")) dutch <- mo_name(microorganisms$fullname, language = "nl") # should be transformable to English again expect_identical(mo_name(dutch, language = NULL), microorganisms$fullname) # gigantic test - will run ALL names # 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(suppressWarnings(mo_ref("Chlamydia psittaci")), "Page, 1968") expect_identical(mo_ref("Chlamydophila psittaci"), "Everett et al., 1999") expect_true(112283007 %in% mo_snomed("Escherichia coli")) # old codes must throw a warning in mo_* family expect_message(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") library(dplyr) expect_equal(example_isolates %>% filter(mo_is_gram_negative()) %>% nrow(), 730) expect_equal(example_isolates %>% filter(mo_is_gram_positive()) %>% nrow(), 1238) expect_equal(example_isolates %>% filter(mo_is_intrinsic_resistant(ab = "Vancomycin")) %>% nrow(), 710) })