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Replace RSI with SIR

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This commit is contained in:
Dr. Matthijs Berends
2023-01-21 23:47:20 +01:00
committed by GitHub
parent 24b12024ce
commit 98e62c9af2
127 changed files with 1746 additions and 1648 deletions
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11
R/mo_property.R
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@ -417,6 +417,8 @@ mo_pathogenicity <- function(x, language = get_AMR_locale(), keep_synonyms = get
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, ...)
metadata <- get_mo_uncertainties()
@ -725,6 +727,8 @@ 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, ...)
metadata <- get_mo_uncertainties()
@ -811,6 +815,8 @@ 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, ... = ...)
metadata <- get_mo_uncertainties()
@ -847,7 +853,7 @@ mo_property <- function(x, property = "fullname", language = get_AMR_locale(), k
x <- find_mo_col(fn = "mo_property")
}
meet_criteria(x, allow_NA = TRUE)
meet_criteria(property, allow_class = "character", has_length = 1, is_in = colnames(AMR_env$MO_lookup))
meet_criteria(property, allow_class = "character", has_length = 1, is_in = colnames(AMR::microorganisms))
language <- validate_language(language)
meet_criteria(keep_synonyms, allow_class = "logical", has_length = 1)
@ -855,7 +861,8 @@ mo_property <- function(x, property = "fullname", language = get_AMR_locale(), k
}
mo_validate <- function(x, property, language, keep_synonyms = keep_synonyms, ...) {
add_MO_lookup_to_AMR_env()
# try to catch an error when inputting an invalid argument
# so the 'call.' can be set to FALSE
tryCatch(x[1L] %in% unlist(AMR_env$MO_lookup[1, property, drop = TRUE]),