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This commit is contained in:
dr. M.S. (Matthijs) Berends
2022-09-18 16:35:45 +02:00
parent 835cf7c32d
commit a20293a0a3
3 changed files with 5 additions and 19 deletions
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16
inst/tinytest/test-data.R
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@ -23,8 +23,6 @@
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# ==================================================================== #
expect_true(AMR:::check_dataset_integrity()) # in misc.R
# IDs should always be unique
expect_identical(nrow(microorganisms), length(unique(microorganisms$mo)))
expect_identical(class(microorganisms$mo), c("mo", "character"))
@ -68,24 +66,12 @@ expect_true(nrow(df[which(df$prevalence == 2), , drop = FALSE]) < nrow(df[which(
expect_true(all(c(
"mo", "fullname",
"kingdom", "phylum", "class", "order", "family", "genus", "species", "subspecies",
"rank", "ref", "species_id", "source", "prevalence", "snomed",
"rank", "ref", "lpsn", "gbif", "status", "source", "prevalence", "snomed",
"kingdom_index", "fullname_lower", "g_species"
) %in% colnames(df)))
expect_true(all(c(
"fullname", "fullname_new", "ref", "prevalence",
"fullname_lower", "g_species"
) %in% colnames(AMR:::MO.old_lookup)))
expect_inherits(AMR:::MO_CONS, "mo")
expect_identical(
class(catalogue_of_life_version()),
c("catalogue_of_life_version", "list")
)
expect_stdout(print(catalogue_of_life_version()))
uncategorised <- subset(
microorganisms,
genus == "Staphylococcus" &