Nothing
# test <- read.csv("tests/testthat/data_baetidae_bold.csv")
test_that("Test checking taxonomic typo", {
test <- read.csv("data_baetidae_bold.csv")
test <- refdb_set_fields_BOLD(test)
test$species_name[10] <- "Baetis aplinus"
test$order_name[5] <- "Ehemeroptera"
res <- refdb_check_tax_typo(test, tol = 1)
expect_equal(sum(sapply(res, length)), 2L)
res <- refdb_check_tax_typo(test, tol = 2)
expect_equal(sum(sapply(res, length)), 4L)
})
test_that("Test checking taxonomic conflicts", {
test <- read.csv("data_baetidae_bold.csv")
test <- refdb_set_fields_BOLD(test)
test$order_name[5] <- "Ehemeroptera"
res <- refdb_check_tax_conflict(test)
# 8L corresponds to conflicts detected above family_name (included)
expect_equal(sum(sapply(res, nrow)), 8L)
})
test_that("Test checking sequence conflicts", {
test <- read.csv("data_baetidae_bold.csv")
test <- refdb_set_fields_BOLD(test)
test$nucleotides[29] <- test$nucleotides[10]
res <- refdb_check_seq_conflict(test)
expect_equal(ncol(res), 3L)
expect_equal(nrow(res), 2L)
})
# test_that("Test reports", {
# test <- read.csv("data_baetidae_bold.csv")
# test_file <- tempfile()
# test <- refdb_set_fields_BOLD(test)
# refdb_report(test, test_file, view = FALSE)
# refdb_report(test, view = FALSE)
# })
test_that("Test refdb_check_seq_homogeneity fails with non aligned sequences", {
test <- read.csv("data_baetidae_bold.csv")
test <- refdb_set_fields_BOLD(test)
expect_error(refdb_check_seq_homogeneity(test, levels = c(species = 0.05)),
"Sequences must be aligned")
})
# test <- read.csv("tests/testthat/data_tocheck_homogeneity.csv")
test_that("Test refdb_check_seq_homogeneity", {
test <- read.csv("data_tocheck_homogeneity.csv")
test <- refdb_set_fields_BOLD(test)
r1 <- refdb_check_seq_homogeneity(test, levels = c(species = 0.05))
r2 <- refdb_check_seq_homogeneity(test, levels = c(genus = 0.1, species = 0.05))
r3 <- refdb_check_seq_homogeneity(test, levels = c(species = 0.05, genus = 0.1))
expect_equal(nrow(r1), 7L)
expect_equal(nrow(r2), 10L)
expect_equal(r2, r3)
})
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