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This commit is contained in:
dr. M.S. (Matthijs) Berends
2023-01-23 15:01:21 +01:00
parent af139a3c82
commit 19fd0ef121
57 changed files with 2864 additions and 2739 deletions
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37
R/mo_property.R
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@ -133,7 +133,6 @@
#' mo_fullname("K. pneu rh")
#' mo_shortname("K. pneu rh")
#'
#'
#' \donttest{
#' # Becker classification, see ?as.mo ----------------------------------------
#'
@ -158,7 +157,7 @@
#' mo_gramstain("Klebsiella pneumoniae", language = "es") # Spanish
#' mo_gramstain("Klebsiella pneumoniae", language = "el") # Greek
#' mo_gramstain("Klebsiella pneumoniae", language = "uk") # Ukrainian
#'
#'
#' # mo_type is equal to mo_kingdom, but mo_kingdom will remain untranslated
#' mo_kingdom("Klebsiella pneumoniae")
#' mo_type("Klebsiella pneumoniae")
@ -426,17 +425,23 @@ 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(
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
)
load_mo_uncertainties(metadata)
out
@ -727,7 +732,7 @@ mo_synonyms <- function(x, language = get_AMR_locale(), keep_synonyms = getOptio
meet_criteria(x, allow_NA = TRUE)
language <- validate_language(language)
meet_criteria(keep_synonyms, allow_class = "logical", has_length = 1)
add_MO_lookup_to_AMR_env()
x.mo <- as.mo(x, language = language, keep_synonyms = keep_synonyms, ...)
@ -815,7 +820,7 @@ mo_url <- function(x, open = FALSE, language = get_AMR_locale(), keep_synonyms =
meet_criteria(open, allow_class = "logical", has_length = 1)
language <- validate_language(language)
meet_criteria(keep_synonyms, allow_class = "logical", has_length = 1)
add_MO_lookup_to_AMR_env()
x.mo <- as.mo(x = x, language = language, keep_synonyms = keep_synonyms, ... = ...)
@ -862,7 +867,7 @@ mo_property <- function(x, property = "fullname", language = get_AMR_locale(), k
mo_validate <- function(x, property, language, keep_synonyms = keep_synonyms, ...) {
add_MO_lookup_to_AMR_env()
# try to catch an error when inputting an invalid argument
# so the 'call.' can be set to FALSE
tryCatch(x[1L] %in% unlist(AMR_env$MO_lookup[1, property, drop = TRUE]),