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(v1.7.1.9051) updated taxonomy, updated git branch name

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dr. M.S. (Matthijs) Berends committed 2021-10-06 13:23:57 +02:00
1 parent 8f5e5a3fc2
commit 37e6e35ec4
139 files changed
+2694 -1862
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inst/tinytest/test-mo.R
+1 -1
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@@ -207,7 +207,7 @@ expect_equal(suppressWarnings(as.character(as.mo("staaur extratest", allow_uncer
expect_message(as.mo("e coli extra_text", allow_uncertain = TRUE))
expect_equal(suppressMessages(as.character(as.mo("unexisting aureus", allow_uncertain = 3))), "B_STPHY_AURS")
expect_equal(suppressMessages(as.character(as.mo("unexisting staphy", allow_uncertain = 3))), "B_STPHY_COPS")
expect_equal(suppressMessages(as.character(as.mo(c("s aur THISISATEST", "Staphylococcus aureus unexisting"), allow_uncertain = 3))), c("B_STPHY_AURS_ANRB", "B_STPHY_AURS_ANRB"))
expect_equal(suppressMessages(as.character(as.mo(c("s aure THISISATEST", "Staphylococcus aureus unexisting"), allow_uncertain = 3))), c("B_STPHY_AURS_AURS", "B_STPHY_AURS_AURS"))
# predefined reference_df
expect_equal(as.character(as.mo("TestingOwnID",
inst/tinytest/test-zzz.R
+3 -1
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@@ -99,7 +99,9 @@ for (i in seq_len(length(import_functions))) {
fn <- names(import_functions)[i]
pkg <- unname(import_functions[i])
# function should exist in foreign pkg namespace
if (AMR:::pkg_is_available(pkg, also_load = FALSE)) {
if (AMR:::pkg_is_available(pkg,
also_load = FALSE,
min_version = if (pkg == "dplyr") "1.0.0" else NULL)) {
tst <- !is.null(AMR:::import_fn(name = fn, pkg = pkg, error_on_fail = FALSE))
expect_true(tst,
info = ifelse(tst,