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breakpoints UTI interpretation fix

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dr. M.S. (Matthijs) Berends
2023-07-10 13:41:52 +02:00
parent 3829311dd3
commit 70c601ca11
28 changed files with 605 additions and 150 deletions
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23
R/mo_property.R
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@ -427,22 +427,13 @@ 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(
ifelse(prev == 1 & kngd == "Bacteria" & rank != "genus",
"Pathogenic",
ifelse(prev < 2 & kngd == "Fungi",
"Potentially pathogenic",
ifelse(prev == 2 & kngd == "Bacteria",
"Non-pathogenic",
ifelse(kngd == "Bacteria",
"Potentially pathogenic",
"Unknown"
)
)
)
),
levels = c("Pathogenic", "Potentially pathogenic", "Non-pathogenic", "Unknown"),
ordered = TRUE
out <- factor(case_when_AMR(prev == 1 & kngd == "Bacteria" & rank != "genus" ~ "Pathogenic",
(prev < 2 & kngd == "Fungi") ~ "Potentially pathogenic",
prev == 2 & kngd == "Bacteria" ~ "Non-pathogenic",
kngd == "Bacteria" ~ "Potentially pathogenic",
TRUE ~ "Unknown"),
levels = c("Pathogenic", "Potentially pathogenic", "Non-pathogenic", "Unknown"),
ordered = TRUE
)
load_mo_uncertainties(metadata)