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Catalogue of Life, replaces ITIS

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dr. M.S. (Matthijs) Berends
2019-02-18 02:33:37 +01:00
parent 9209787a53
commit 54f8258f8c
88 changed files with 607 additions and 590 deletions
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14
tests/testthat/test-mo_property.R
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@ -23,31 +23,29 @@ context("mo_property.R")
test_that("mo_property works", {
expect_equal(mo_kingdom("E. coli"), "Bacteria")
expect_equal(mo_subkingdom("E. coli"), "Negibacteria")
expect_equal(mo_phylum("E. coli"), "Proteobacteria")
expect_equal(mo_class("E. coli"), "Gammaproteobacteria")
expect_equal(mo_order("E. coli"), "Enterobacteriales")
expect_equal(mo_family("E. coli"), "Enterobacteriaceae")
expect_equal(mo_genus("E. coli"), "Escherichia")
expect_equal(mo_species("E. coli"), "coli")
expect_equal(mo_subspecies("E. coli"), NA_character_)
expect_equal(mo_subspecies("E. coli"), "")
expect_equal(mo_fullname("E. coli"), "Escherichia coli")
expect_equal(mo_type("E. coli", language = "en"), "Bacteria")
expect_equal(mo_gramstain("E. coli", language = "en"), "Gram negative")
expect_equal(mo_TSN("E. coli"), 285)
expect_equal(class(mo_taxonomy("E. coli")), "list")
expect_equal(names(mo_taxonomy("E. coli")), c("kingdom", "subkingdom", "phylum", "class", "order",
expect_equal(names(mo_taxonomy("E. coli")), c("kingdom", "phylum", "class", "order",
"family", "genus", "species", "subspecies"))
expect_equal(mo_ref("E. coli"), "Castellani and Chalmers, 1919")
expect_equal(mo_authors("E. coli"), "Castellani and Chalmers")
expect_equal(mo_ref("E. coli"), "(Migula, 1895) Castellani and Chalmers, 1919")
expect_equal(mo_authors("E. coli"), "(Migula) Castellani and Chalmers")
expect_equal(mo_year("E. coli"), 1919)
expect_equal(mo_shortname("MRSA"), "S. aureus")
expect_equal(mo_shortname("MRSA", Becker = TRUE), "S. aureus")
expect_equal(mo_shortname("MRSA", Becker = "all", language = "en"), "CoPS")
expect_equal(mo_shortname("S. aga"), "S. agalactiae")
expect_equal(mo_shortname("S. aga", Lancefield = TRUE), "GBS")
expect_equal(mo_shortname("S. agalac"), "S. agalactiae")
expect_equal(mo_shortname("S. agalac", Lancefield = TRUE), "GBS")
# test integrity
MOs <- AMR::microorganisms