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(v2.1.1.9082) algorithm updates

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2024-09-30 18:46:55 +02:00
parent ac1c40d8bb
commit 681fe011fe
25 changed files with 15593 additions and 15505 deletions
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26
data-raw/_pre_commit_checks.R
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@ -158,6 +158,32 @@ pre_commit_lst$MO_STREP_ABCG <- AMR::microorganisms$mo[which(AMR::microorganisms
"group a", "group b", "group c", "group g"
))]
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$MO_WHO_PRIORITY_GENERA <- c(
# World Health Organization's (WHO) Priority Pathogen List
"Acinetobacter",
"Aspergillus",
"Blastomyces",
"Campylobacter",
"Candida",
"Clostridioides",
"Coccidioides",
"Cryptococcus",
"Enterococcus",
"Fusarium",
"Haemophilus",
"Helicobacter",
"Histoplasma",
"Klebsiella",
"Mycobacterium",
"Neisseria",
"Paracoccidioides",
"Pneumocystis",
"Pseudomonas",
"Salmonella",
"Shigella",
"Staphylococcus",
"Streptococcus"
)
pre_commit_lst$MO_RELEVANT_GENERA <- c(
"Absidia",
"Acanthamoeba",