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(v2.1.1.9087) update unit tests
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@ -159,15 +159,18 @@ pre_commit_lst$MO_STREP_ABCG <- AMR::microorganisms$mo[which(AMR::microorganisms
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))]
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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(_|$)|B_STRPT_SLVR(_|$))")]
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pre_commit_lst$MO_WHO_PRIORITY_GENERA <- c(
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# World Health Organization's (WHO) Priority Pathogen List
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# World Health Organization's (WHO) Priority Pathogen List (some are from the group Enterobacteriaceae)
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"Acinetobacter",
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"Aspergillus",
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"Blastomyces",
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"Campylobacter",
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"Candida",
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"Citrobacter",
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"Clostridioides",
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"Coccidioides",
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"Cryptococcus",
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"Edwardsiella",
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"Enterobacter",
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"Enterococcus",
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"Escherichia",
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"Fusarium",
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@ -175,15 +178,20 @@ pre_commit_lst$MO_WHO_PRIORITY_GENERA <- c(
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"Helicobacter",
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"Histoplasma",
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"Klebsiella",
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"Morganella",
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"Mycobacterium",
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"Neisseria",
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"Paracoccidioides",
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"Pneumocystis",
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"Proteus",
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"Providencia",
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"Pseudomonas",
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"Salmonella",
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"Serratia",
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"Shigella",
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"Staphylococcus",
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"Streptococcus"
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"Streptococcus",
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"Yersinia"
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)
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pre_commit_lst$MO_RELEVANT_GENERA <- c(
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"Absidia",
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