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styled, unit test fix
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228
R/mo_property.R
228
R/mo_property.R
@ -42,15 +42,15 @@
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#' Since the top-level of the taxonomy is sometimes referred to as 'kingdom' and sometimes as 'domain', the functions [mo_kingdom()] and [mo_domain()] return the exact same results.
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#'
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#' The Gram stain - [mo_gramstain()] - will be determined based on the taxonomic kingdom and phylum. According to Cavalier-Smith (2002, [PMID 11837318](https://pubmed.ncbi.nlm.nih.gov/11837318)), who defined subkingdoms Negibacteria and Posibacteria, only these phyla are Posibacteria: Actinobacteria, Chloroflexi, Firmicutes and Tenericutes. These bacteria are considered Gram-positive, except for members of the class Negativicutes which are Gram-negative. Members of other bacterial phyla are all considered Gram-negative. Species outside the kingdom of Bacteria will return a value `NA`. Functions [mo_is_gram_negative()] and [mo_is_gram_positive()] always return `TRUE` or `FALSE` (except when the input is `NA` or the MO code is `UNKNOWN`), thus always return `FALSE` for species outside the taxonomic kingdom of Bacteria.
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#'
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#'
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#' Determination of yeasts - [mo_is_yeast()] - will be based on the taxonomic kingdom and class. *Budding yeasts* are fungi of the phylum Ascomycetes, class Saccharomycetes (also called Hemiascomycetes). *True yeasts* are aggregated into the underlying order Saccharomycetales. Thus, for all microorganisms that are fungi and member of the taxonomic class Saccharomycetes, the function will return `TRUE`. It returns `FALSE` otherwise (except when the input is `NA` or the MO code is `UNKNOWN`).
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#'
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#'
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#' Intrinsic resistance - [mo_is_intrinsic_resistant()] - will be determined based on the [intrinsic_resistant] data set, which is based on `r format_eucast_version_nr(3.3)`. The [mo_is_intrinsic_resistant()] functions can be vectorised over arguments `x` (input for microorganisms) and over `ab` (input for antibiotics).
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#'
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#' All output [will be translated][translate] where possible.
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#'
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#' The function [mo_url()] will return the direct URL to the online database entry, which also shows the scientific reference of the concerned species.
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#'
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#'
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#' SNOMED codes - [mo_snomed()] - are from the `r SNOMED_VERSION$current_source`. See *Source* and the [microorganisms] data set for more info.
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#' @inheritSection mo_matching_score Matching Score for Microorganisms
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#' @inheritSection catalogue_of_life Catalogue of Life
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@ -139,30 +139,32 @@
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#' mo_type("Klebsiella pneumoniae")
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#'
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#' mo_fullname("S. pyogenes",
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#' Lancefield = TRUE,
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#' language = "de")
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#' Lancefield = TRUE,
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#' language = "de"
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#' )
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#' mo_fullname("S. pyogenes",
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#' Lancefield = TRUE,
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#' language = "nl")
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#' Lancefield = TRUE,
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#' language = "nl"
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#' )
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#'
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#'
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#' # other --------------------------------------------------------------------
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#'
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#'
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#' mo_is_yeast(c("Candida", "Trichophyton", "Klebsiella"))
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#'
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#'
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#' # gram stains and intrinsic resistance can be used as a filter in dplyr verbs
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#' if (require("dplyr")) {
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#' example_isolates %>%
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#' filter(mo_is_gram_positive())
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#'
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#'
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#' example_isolates %>%
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#' filter(mo_is_intrinsic_resistant(ab = "vanco"))
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#' }
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#'
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#'
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#'
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#'
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#' # get a list with the complete taxonomy (from kingdom to subspecies)
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#' mo_taxonomy("Klebsiella pneumoniae")
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#'
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#'
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#' # get a list with the taxonomy, the authors, Gram-stain,
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#' # SNOMED codes, and URL to the online database
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#' mo_info("Klebsiella pneumoniae")
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@ -174,11 +176,12 @@ mo_name <- function(x, language = get_AMR_locale(), ...) {
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}
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meet_criteria(x, allow_NA = TRUE)
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meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
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translate_into_language(mo_validate(x = x, property = "fullname", language = language, ...),
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language = language,
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only_unknown = FALSE,
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only_affect_mo_names = TRUE)
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language = language,
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only_unknown = FALSE,
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only_affect_mo_names = TRUE
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)
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}
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#' @rdname mo_property
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@ -194,20 +197,20 @@ mo_shortname <- function(x, language = get_AMR_locale(), ...) {
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}
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meet_criteria(x, allow_NA = TRUE)
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meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
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x.mo <- as.mo(x, language = language, ...)
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metadata <- get_mo_failures_uncertainties_renamed()
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replace_empty <- function(x) {
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x[x == ""] <- "spp."
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x
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}
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# get first char of genus and complete species in English
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genera <- mo_genus(x.mo, language = NULL)
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shortnames <- paste0(substr(genera, 1, 1), ". ", replace_empty(mo_species(x.mo, language = NULL)))
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# exceptions for where no species is known
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shortnames[shortnames %like% ".[.] spp[.]"] <- genera[shortnames %like% ".[.] spp[.]"]
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# exceptions for staphylococci
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@ -217,7 +220,7 @@ mo_shortname <- function(x, language = get_AMR_locale(), ...) {
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shortnames[shortnames %like% "S. group [ABCDFGHK]"] <- paste0("G", gsub("S. group ([ABCDFGHK])", "\\1", shortnames[shortnames %like% "S. group [ABCDFGHK]"], perl = TRUE), "S")
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# unknown species etc.
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shortnames[shortnames %like% "unknown"] <- paste0("(", trimws(gsub("[^a-zA-Z -]", "", shortnames[shortnames %like% "unknown"], perl = TRUE)), ")")
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shortnames[is.na(x.mo)] <- NA_character_
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load_mo_failures_uncertainties_renamed(metadata)
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translate_into_language(shortnames, language = language, only_unknown = FALSE, only_affect_mo_names = TRUE)
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@ -234,7 +237,7 @@ mo_subspecies <- function(x, language = get_AMR_locale(), ...) {
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}
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meet_criteria(x, allow_NA = TRUE)
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meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
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translate_into_language(mo_validate(x = x, property = "subspecies", language = language, ...), language = language, only_unknown = TRUE)
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}
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@ -247,7 +250,7 @@ mo_species <- function(x, language = get_AMR_locale(), ...) {
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}
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meet_criteria(x, allow_NA = TRUE)
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meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
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translate_into_language(mo_validate(x = x, property = "species", language = language, ...), language = language, only_unknown = TRUE)
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}
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@ -260,7 +263,7 @@ mo_genus <- function(x, language = get_AMR_locale(), ...) {
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}
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meet_criteria(x, allow_NA = TRUE)
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meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
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translate_into_language(mo_validate(x = x, property = "genus", language = language, ...), language = language, only_unknown = TRUE)
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}
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@ -273,7 +276,7 @@ mo_family <- function(x, language = get_AMR_locale(), ...) {
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}
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meet_criteria(x, allow_NA = TRUE)
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meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
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translate_into_language(mo_validate(x = x, property = "family", language = language, ...), language = language, only_unknown = TRUE)
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}
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@ -286,7 +289,7 @@ mo_order <- function(x, language = get_AMR_locale(), ...) {
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}
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meet_criteria(x, allow_NA = TRUE)
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meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
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translate_into_language(mo_validate(x = x, property = "order", language = language, ...), language = language, only_unknown = TRUE)
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}
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@ -299,7 +302,7 @@ mo_class <- function(x, language = get_AMR_locale(), ...) {
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}
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meet_criteria(x, allow_NA = TRUE)
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meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
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translate_into_language(mo_validate(x = x, property = "class", language = language, ...), language = language, only_unknown = TRUE)
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}
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@ -312,7 +315,7 @@ mo_phylum <- function(x, language = get_AMR_locale(), ...) {
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}
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meet_criteria(x, allow_NA = TRUE)
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meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
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translate_into_language(mo_validate(x = x, property = "phylum", language = language, ...), language = language, only_unknown = TRUE)
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}
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@ -325,7 +328,7 @@ mo_kingdom <- function(x, language = get_AMR_locale(), ...) {
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}
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meet_criteria(x, allow_NA = TRUE)
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meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
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translate_into_language(mo_validate(x = x, property = "kingdom", language = language, ...), language = language, only_unknown = TRUE)
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}
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@ -342,7 +345,7 @@ mo_type <- function(x, language = get_AMR_locale(), ...) {
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}
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meet_criteria(x, allow_NA = TRUE)
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meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
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x.mo <- as.mo(x, language = language, ...)
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out <- mo_kingdom(x.mo, language = NULL)
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out[which(mo_is_yeast(x.mo))] <- "Yeasts"
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@ -358,24 +361,26 @@ mo_gramstain <- function(x, language = get_AMR_locale(), ...) {
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}
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meet_criteria(x, allow_NA = TRUE)
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meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
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x.mo <- as.mo(x, language = language, ...)
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metadata <- get_mo_failures_uncertainties_renamed()
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x <- rep(NA_character_, length(x))
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# make all bacteria Gram negative
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x[mo_kingdom(x.mo) == "Bacteria"] <- "Gram-negative"
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# overwrite these 4 phyla with Gram-positives
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# Source: https://itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=956097 (Cavalier-Smith, 2002)
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x[(mo_phylum(x.mo) %in% c("Actinobacteria",
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"Chloroflexi",
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"Firmicutes",
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"Tenericutes") &
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# but class Negativicutes (of phylum Firmicutes) are Gram-negative!
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mo_class(x.mo) != "Negativicutes")
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# and of course our own ID for Gram-positives
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| x.mo == "B_GRAMP"] <- "Gram-positive"
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x[(mo_phylum(x.mo) %in% c(
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"Actinobacteria",
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"Chloroflexi",
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"Firmicutes",
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"Tenericutes"
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) &
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# but class Negativicutes (of phylum Firmicutes) are Gram-negative!
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mo_class(x.mo) != "Negativicutes")
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# and of course our own ID for Gram-positives
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| x.mo == "B_GRAMP"] <- "Gram-positive"
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load_mo_failures_uncertainties_renamed(metadata)
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translate_into_language(x, language = language, only_unknown = FALSE)
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}
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@ -389,7 +394,7 @@ mo_is_gram_negative <- function(x, language = get_AMR_locale(), ...) {
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}
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meet_criteria(x, allow_NA = TRUE)
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meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
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x.mo <- as.mo(x, language = language, ...)
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metadata <- get_mo_failures_uncertainties_renamed()
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grams <- mo_gramstain(x.mo, language = NULL)
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@ -408,7 +413,7 @@ mo_is_gram_positive <- function(x, language = get_AMR_locale(), ...) {
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}
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meet_criteria(x, allow_NA = TRUE)
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meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
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x.mo <- as.mo(x, language = language, ...)
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metadata <- get_mo_failures_uncertainties_renamed()
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grams <- mo_gramstain(x.mo, language = NULL)
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@ -427,15 +432,15 @@ mo_is_yeast <- function(x, language = get_AMR_locale(), ...) {
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}
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meet_criteria(x, allow_NA = TRUE)
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meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
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x.mo <- as.mo(x, language = language, ...)
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metadata <- get_mo_failures_uncertainties_renamed()
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x.kingdom <- mo_kingdom(x.mo, language = NULL)
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x.class <- mo_class(x.mo, language = NULL)
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load_mo_failures_uncertainties_renamed(metadata)
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out <- rep(FALSE, length(x))
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out[x.kingdom == "Fungi" & x.class == "Saccharomycetes"] <- TRUE
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out[x.mo %in% c(NA_character_, "UNKNOWN")] <- NA
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@ -452,10 +457,10 @@ mo_is_intrinsic_resistant <- function(x, ab, language = get_AMR_locale(), ...) {
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meet_criteria(x, allow_NA = TRUE)
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meet_criteria(ab, allow_NA = FALSE)
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meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
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x <- as.mo(x, language = language, ...)
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ab <- as.ab(ab, language = NULL, flag_multiple_results = FALSE, info = FALSE)
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if (length(x) == 1 & length(ab) > 1) {
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x <- rep(x, length(ab))
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} else if (length(ab) == 1 & length(x) > 1) {
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@ -464,14 +469,16 @@ mo_is_intrinsic_resistant <- function(x, ab, language = get_AMR_locale(), ...) {
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if (length(x) != length(ab)) {
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stop_("length of `x` and `ab` must be equal, or one of them must be of length 1.")
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}
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# show used version number once per session (pkg_env will reload every session)
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if (message_not_thrown_before("mo_is_intrinsic_resistant", "version.mo", entire_session = TRUE)) {
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message_("Determining intrinsic resistance based on ",
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format_eucast_version_nr(3.3, markdown = FALSE), ". ",
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font_red("This note will be shown once per session."))
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message_(
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"Determining intrinsic resistance based on ",
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format_eucast_version_nr(3.3, markdown = FALSE), ". ",
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font_red("This note will be shown once per session.")
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)
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}
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# runs against internal vector: INTRINSIC_R (see zzz.R)
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paste(x, ab) %in% INTRINSIC_R
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}
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@ -485,7 +492,7 @@ mo_snomed <- function(x, language = get_AMR_locale(), ...) {
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}
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meet_criteria(x, allow_NA = TRUE)
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meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
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mo_validate(x = x, property = "snomed", language = language, ...)
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}
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@ -498,7 +505,7 @@ mo_ref <- function(x, language = get_AMR_locale(), ...) {
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}
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meet_criteria(x, allow_NA = TRUE)
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meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
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mo_validate(x = x, property = "ref", language = language, ...)
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}
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@ -511,7 +518,7 @@ mo_authors <- function(x, language = get_AMR_locale(), ...) {
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}
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meet_criteria(x, allow_NA = TRUE)
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meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
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x <- mo_validate(x = x, property = "ref", language = language, ...)
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# remove last 4 digits and presumably the comma and space that preceed them
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x[!is.na(x)] <- gsub(",? ?[0-9]{4}", "", x[!is.na(x)], perl = TRUE)
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@ -527,7 +534,7 @@ mo_year <- function(x, language = get_AMR_locale(), ...) {
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}
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meet_criteria(x, allow_NA = TRUE)
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meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
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x <- mo_validate(x = x, property = "ref", language = language, ...)
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# get last 4 digits
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x[!is.na(x)] <- gsub(".*([0-9]{4})$", "\\1", x[!is.na(x)], perl = TRUE)
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@ -543,7 +550,7 @@ mo_lpsn <- function(x, language = get_AMR_locale(), ...) {
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}
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meet_criteria(x, allow_NA = TRUE)
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meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
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mo_validate(x = x, property = "species_id", language = language, ...)
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}
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@ -556,32 +563,34 @@ mo_rank <- function(x, language = get_AMR_locale(), ...) {
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}
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meet_criteria(x, allow_NA = TRUE)
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meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
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mo_validate(x = x, property = "rank", language = language, ...)
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}
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#' @rdname mo_property
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#' @export
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mo_taxonomy <- function(x, language = get_AMR_locale(), ...) {
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mo_taxonomy <- function(x, language = get_AMR_locale(), ...) {
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if (missing(x)) {
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# this tries to find the data and an <mo> column
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x <- find_mo_col(fn = "mo_taxonomy")
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}
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meet_criteria(x, allow_NA = TRUE)
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meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
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x <- as.mo(x, language = language, ...)
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metadata <- get_mo_failures_uncertainties_renamed()
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out <- list(kingdom = mo_kingdom(x, language = language),
|
||||
phylum = mo_phylum(x, language = language),
|
||||
class = mo_class(x, language = language),
|
||||
order = mo_order(x, language = language),
|
||||
family = mo_family(x, language = language),
|
||||
genus = mo_genus(x, language = language),
|
||||
species = mo_species(x, language = language),
|
||||
subspecies = mo_subspecies(x, language = language))
|
||||
|
||||
|
||||
out <- list(
|
||||
kingdom = mo_kingdom(x, language = language),
|
||||
phylum = mo_phylum(x, language = language),
|
||||
class = mo_class(x, language = language),
|
||||
order = mo_order(x, language = language),
|
||||
family = mo_family(x, language = language),
|
||||
genus = mo_genus(x, language = language),
|
||||
species = mo_species(x, language = language),
|
||||
subspecies = mo_subspecies(x, language = language)
|
||||
)
|
||||
|
||||
load_mo_failures_uncertainties_renamed(metadata)
|
||||
out
|
||||
}
|
||||
@ -595,10 +604,10 @@ mo_synonyms <- function(x, language = get_AMR_locale(), ...) {
|
||||
}
|
||||
meet_criteria(x, allow_NA = TRUE)
|
||||
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
|
||||
|
||||
|
||||
x <- as.mo(x, language = language, ...)
|
||||
metadata <- get_mo_failures_uncertainties_renamed()
|
||||
|
||||
|
||||
IDs <- mo_name(x = x, language = NULL)
|
||||
syns <- lapply(IDs, function(newname) {
|
||||
res <- sort(microorganisms.old[which(microorganisms.old$fullname_new == newname), "fullname", drop = TRUE])
|
||||
@ -614,38 +623,43 @@ mo_synonyms <- function(x, language = get_AMR_locale(), ...) {
|
||||
} else {
|
||||
result <- unlist(syns)
|
||||
}
|
||||
|
||||
|
||||
load_mo_failures_uncertainties_renamed(metadata)
|
||||
result
|
||||
}
|
||||
|
||||
#' @rdname mo_property
|
||||
#' @export
|
||||
mo_info <- function(x, language = get_AMR_locale(), ...) {
|
||||
mo_info <- function(x, language = get_AMR_locale(), ...) {
|
||||
if (missing(x)) {
|
||||
# this tries to find the data and an <mo> column
|
||||
x <- find_mo_col(fn = "mo_info")
|
||||
}
|
||||
meet_criteria(x, allow_NA = TRUE)
|
||||
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
|
||||
|
||||
|
||||
x <- as.mo(x, language = language, ...)
|
||||
metadata <- get_mo_failures_uncertainties_renamed()
|
||||
|
||||
info <- lapply(x, function(y)
|
||||
c(mo_taxonomy(y, language = language),
|
||||
list(synonyms = mo_synonyms(y),
|
||||
gramstain = mo_gramstain(y, language = language),
|
||||
url = unname(mo_url(y, open = FALSE)),
|
||||
ref = mo_ref(y),
|
||||
snomed = unlist(mo_snomed(y)))))
|
||||
|
||||
info <- lapply(x, function(y) {
|
||||
c(
|
||||
mo_taxonomy(y, language = language),
|
||||
list(
|
||||
synonyms = mo_synonyms(y),
|
||||
gramstain = mo_gramstain(y, language = language),
|
||||
url = unname(mo_url(y, open = FALSE)),
|
||||
ref = mo_ref(y),
|
||||
snomed = unlist(mo_snomed(y))
|
||||
)
|
||||
)
|
||||
})
|
||||
if (length(info) > 1) {
|
||||
names(info) <- mo_name(x)
|
||||
result <- info
|
||||
} else {
|
||||
result <- info[[1L]]
|
||||
}
|
||||
|
||||
|
||||
load_mo_failures_uncertainties_renamed(metadata)
|
||||
result
|
||||
}
|
||||
@ -660,30 +674,31 @@ mo_url <- function(x, open = FALSE, language = get_AMR_locale(), ...) {
|
||||
meet_criteria(x, allow_NA = TRUE)
|
||||
meet_criteria(open, allow_class = "logical", has_length = 1)
|
||||
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
|
||||
|
||||
|
||||
x.mo <- as.mo(x = x, language = language, ... = ...)
|
||||
metadata <- get_mo_failures_uncertainties_renamed()
|
||||
|
||||
|
||||
df <- microorganisms[match(x.mo, microorganisms$mo), c("mo", "fullname", "source", "kingdom", "rank"), drop = FALSE]
|
||||
df$url <- ifelse(df$source == "LPSN",
|
||||
paste0(CATALOGUE_OF_LIFE$url_LPSN, "/species/", gsub(" ", "-", tolower(df$fullname), fixed = TRUE)),
|
||||
paste0(CATALOGUE_OF_LIFE$url_CoL, "/data/search?type=EXACT&q=", gsub(" ", "%20", df$fullname, fixed = TRUE)))
|
||||
|
||||
paste0(CATALOGUE_OF_LIFE$url_LPSN, "/species/", gsub(" ", "-", tolower(df$fullname), fixed = TRUE)),
|
||||
paste0(CATALOGUE_OF_LIFE$url_CoL, "/data/search?type=EXACT&q=", gsub(" ", "%20", df$fullname, fixed = TRUE))
|
||||
)
|
||||
|
||||
genera <- which(df$kingdom == "Bacteria" & df$rank == "genus")
|
||||
df$url[genera] <- gsub("/species/", "/genus/", df$url[genera], fixed = TRUE)
|
||||
subsp <- which(df$kingdom == "Bacteria" & df$rank %in% c("subsp.", "infraspecies"))
|
||||
df$url[subsp] <- gsub("/species/", "/subspecies/", df$url[subsp], fixed = TRUE)
|
||||
|
||||
|
||||
u <- df$url
|
||||
names(u) <- df$fullname
|
||||
|
||||
|
||||
if (isTRUE(open)) {
|
||||
if (length(u) > 1) {
|
||||
warning_("in `mo_url()`: only the first URL will be opened, as `browseURL()` only suports one string.")
|
||||
}
|
||||
utils::browseURL(u[1L])
|
||||
}
|
||||
|
||||
|
||||
load_mo_failures_uncertainties_renamed(metadata)
|
||||
u
|
||||
}
|
||||
@ -699,7 +714,7 @@ mo_property <- function(x, property = "fullname", language = get_AMR_locale(), .
|
||||
meet_criteria(x, allow_NA = TRUE)
|
||||
meet_criteria(property, allow_class = "character", has_length = 1, is_in = colnames(microorganisms))
|
||||
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
|
||||
|
||||
|
||||
translate_into_language(mo_validate(x = x, property = property, language = language, ...), language = language, only_unknown = TRUE)
|
||||
}
|
||||
|
||||
@ -715,22 +730,22 @@ mo_validate <- function(x, property, language, ...) {
|
||||
Lancefield <- FALSE
|
||||
}
|
||||
has_Becker_or_Lancefield <- Becker %in% c(TRUE, "all") | Lancefield %in% c(TRUE, "all")
|
||||
|
||||
|
||||
if (tryCatch(all(x[!is.na(x)] %in% MO_lookup$mo) & !has_Becker_or_Lancefield, error = function(e) FALSE)) {
|
||||
# special case for mo_* functions where class is already <mo>
|
||||
x <- MO_lookup[match(x, MO_lookup$mo), property, drop = TRUE]
|
||||
|
||||
} else {
|
||||
# try to catch an error when inputting an invalid argument
|
||||
# so the 'call.' can be set to FALSE
|
||||
tryCatch(x[1L] %in% MO_lookup[1, property, drop = TRUE],
|
||||
error = function(e) stop(e$message, call. = FALSE))
|
||||
|
||||
error = function(e) stop(e$message, call. = FALSE)
|
||||
)
|
||||
|
||||
if (!all(x[!is.na(x)] %in% MO_lookup[, property, drop = TRUE]) | has_Becker_or_Lancefield) {
|
||||
x <- exec_as.mo(x, property = property, language = language, ...)
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
if (property == "mo") {
|
||||
return(set_clean_class(x, new_class = c("mo", "character")))
|
||||
} else if (property == "species_id") {
|
||||
@ -747,9 +762,12 @@ find_mo_col <- function(fn) {
|
||||
# which is useful when functions are used within dplyr verbs
|
||||
df <- get_current_data(arg_name = "x", call = -3) # will return an error if not found
|
||||
mo <- NULL
|
||||
try({
|
||||
mo <- suppressMessages(search_type_in_df(df, "mo"))
|
||||
}, silent = TRUE)
|
||||
try(
|
||||
{
|
||||
mo <- suppressMessages(search_type_in_df(df, "mo"))
|
||||
},
|
||||
silent = TRUE
|
||||
)
|
||||
if (!is.null(df) && !is.null(mo) && is.data.frame(df)) {
|
||||
if (message_not_thrown_before(fn = fn)) {
|
||||
message_("Using column '", font_bold(mo), "' as input for `", fn, "()`")
|
||||
|
||||
Reference in New Issue
Block a user