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Updated mo_gramstain() to reflect current taxonomy, fixes #83

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dr. M.S. (Matthijs) Berends
2022-12-09 10:30:25 +01:00
parent 6017f81e74
commit 510140fc55
5 changed files with 51 additions and 11 deletions
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40
inst/tinytest/test-mo_property.R
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@ -44,6 +44,43 @@ expect_equal(mo_shortname("Staphylococcus aureus", Becker = "all", language = "e
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$phylum, na.rm = TRUE))
current_grampos_classes <- c(
"",
"Acidimicrobiia",
"Actinomycetes",
"Anaerolineae",
"Ardenticatenia",
"Bacilli",
"Caldilineae",
"Chloroflexia",
"Clostridia",
"Coriobacteriia",
"Culicoidibacteria",
"Dehalococcoidia",
"Erysipelotrichia",
"Ktedonobacteria",
"Limnochordia",
"Mollicutes",
"Negativicutes",
"Nitriliruptoria",
"Rubrobacteria",
"Tepidiformia",
"Thermoflexia",
"Thermoleophilia",
"Thermolithobacteria",
"Tissierellia"
)
expect_identical(sort(unique(microorganisms[which(microorganisms$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")
@ -72,8 +109,7 @@ expect_true(mo_url("Candida albicans") %like% "gbif.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", keep_synonyms = TRUE))
expect_identical(microorganisms$fullname, mo_fullname(microorganisms$fullname, language = "en", keep_synonyms = TRUE))
# check languages
expect_equal(mo_type("Escherichia coli", language = "de"), "Bakterien")