P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-08-19 12:22:10 +02:00
Code Releases Activity

new mo_cleaning_regex

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2022-10-04 11:20:58 +02:00
parent a62ff0a1b9
commit 082e52a0dd
10 changed files with 80 additions and 148 deletions
Download Patch File Download Diff File Expand all files Collapse all files

13
inst/tinytest/test-mo.R
View File

@@ -232,14 +232,6 @@ expect_equal(suppressMessages(as.character(as.mo("Escherichia blattae"))), "B_SH
expect_equal(suppressMessages(as.character(as.mo(c("E. coli", "Chlamydo psittaci")))), c("B_ESCHR_COLI", "B_CHLMY_PSTT"))
expect_equal(suppressMessages(mo_name("eubcom")), "Clostridium combesii")
# check uncertain names
expect_equal(suppressMessages(as.character(as.mo("staaur extratest", allow_uncertain = TRUE))), "B_STPHY_AURS")
expect_equal(suppressWarnings(as.character(as.mo("staaur extratest", allow_uncertain = FALSE))), "UNKNOWN")
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 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",
@@ -311,11 +303,6 @@ expect_equal(
rep("UNKNOWN", 3)
)
expect_error(translate_allow_uncertain(5))
# debug mode
expect_stdout(print(suppressMessages(suppressWarnings(as.mo("kshgcjkhsdgkshjdfsfvsdfv", debug = TRUE, allow_uncertain = 3)))))
# ..coccus
expect_equal(
as.character(as.mo(c("meningococ", "gonococ", "pneumococ"))),