mirror of
https://github.com/msberends/AMR.git
synced 2025-07-10 21:01:57 +02:00
(v2.1.1.9082) algorithm updates
This commit is contained in:
@ -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",
|
||||
|
Reference in New Issue
Block a user