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(v2.1.1.9087) update unit tests

This commit is contained in:
2024-10-04 15:28:44 +02:00
parent 738689beea
commit 9fb891eee2
5 changed files with 34272 additions and 7 deletions

View File

@ -159,15 +159,18 @@ pre_commit_lst$MO_STREP_ABCG <- AMR::microorganisms$mo[which(AMR::microorganisms
))]
pre_commit_lst$MO_LANCEFIELD <- AMR::microorganisms$mo[which(AMR::microorganisms$mo %like% "^(B_STRPT_PYGN(_|$)|B_STRPT_AGLC(_|$)|B_STRPT_(DYSG|EQUI)(_|$)|B_STRPT_ANGN(_|$)|B_STRPT_(DYSG|CANS)(_|$)|B_STRPT_SNGN(_|$)|B_STRPT_SLVR(_|$))")]
pre_commit_lst$MO_WHO_PRIORITY_GENERA <- c(
# World Health Organization's (WHO) Priority Pathogen List
# World Health Organization's (WHO) Priority Pathogen List (some are from the group Enterobacteriaceae)
"Acinetobacter",
"Aspergillus",
"Blastomyces",
"Campylobacter",
"Candida",
"Citrobacter",
"Clostridioides",
"Coccidioides",
"Cryptococcus",
"Edwardsiella",
"Enterobacter",
"Enterococcus",
"Escherichia",
"Fusarium",
@ -175,15 +178,20 @@ pre_commit_lst$MO_WHO_PRIORITY_GENERA <- c(
"Helicobacter",
"Histoplasma",
"Klebsiella",
"Morganella",
"Mycobacterium",
"Neisseria",
"Paracoccidioides",
"Pneumocystis",
"Proteus",
"Providencia",
"Pseudomonas",
"Salmonella",
"Serratia",
"Shigella",
"Staphylococcus",
"Streptococcus"
"Streptococcus",
"Yersinia"
)
pre_commit_lst$MO_RELEVANT_GENERA <- c(
"Absidia",