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(v2.1.1.9082) algorithm updates

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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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4
R/mo_property.R
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@ -442,8 +442,8 @@ mo_pathogenicity <- function(x, language = get_AMR_locale(), keep_synonyms = get
kngd <- AMR_env$MO_lookup$kingdom[match(x.mo, AMR_env$MO_lookup$mo)]
rank <- AMR_env$MO_lookup$rank[match(x.mo, AMR_env$MO_lookup$mo)]
out <- factor(case_when_AMR(prev == 1 & kngd == "Bacteria" & rank != "genus" ~ "Pathogenic",
(prev < 2 & kngd == "Fungi") ~ "Potentially pathogenic",
out <- factor(case_when_AMR(prev <= 1.15 & kngd == "Bacteria" & rank != "genus" ~ "Pathogenic",
prev < 2 & kngd == "Fungi" ~ "Potentially pathogenic",
prev == 2 & kngd == "Bacteria" ~ "Non-pathogenic",
kngd == "Bacteria" ~ "Potentially pathogenic",
TRUE ~ "Unknown"),