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(v0.9.0.9023) EUCAST 2020 guidelines
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@ -145,7 +145,7 @@ mo_fullname <- mo_name
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#' @rdname mo_property
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#' @export
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mo_shortname <- function(x, language = get_locale(), ...) {
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x.mo <- AMR::as.mo(x, ...)
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x.mo <- as.mo(x, ...)
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metadata <- get_mo_failures_uncertainties_renamed()
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replace_empty <- function(x) {
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@ -223,7 +223,7 @@ mo_type <- function(x, language = get_locale(), ...) {
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#' @rdname mo_property
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#' @export
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mo_gramstain <- function(x, language = get_locale(), ...) {
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x.mo <- AMR::as.mo(x, ...)
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x.mo <- as.mo(x, ...)
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metadata <- get_mo_failures_uncertainties_renamed()
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x.phylum <- mo_phylum(x.mo)
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@ -290,17 +290,17 @@ mo_rank <- function(x, ...) {
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#' @rdname mo_property
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#' @export
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mo_taxonomy <- function(x, language = get_locale(), ...) {
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x <- AMR::as.mo(x, ...)
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x <- as.mo(x, ...)
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metadata <- get_mo_failures_uncertainties_renamed()
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result <- base::list(kingdom = AMR::mo_kingdom(x, language = language),
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phylum = AMR::mo_phylum(x, language = language),
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class = AMR::mo_class(x, language = language),
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order = AMR::mo_order(x, language = language),
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family = AMR::mo_family(x, language = language),
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genus = AMR::mo_genus(x, language = language),
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species = AMR::mo_species(x, language = language),
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subspecies = AMR::mo_subspecies(x, language = language))
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result <- base::list(kingdom = mo_kingdom(x, language = language),
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phylum = mo_phylum(x, language = language),
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class = mo_class(x, language = language),
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order = mo_order(x, language = language),
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family = mo_family(x, language = language),
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genus = mo_genus(x, language = language),
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species = mo_species(x, language = language),
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subspecies = mo_subspecies(x, language = language))
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load_mo_failures_uncertainties_renamed(metadata)
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result
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@ -309,12 +309,12 @@ mo_taxonomy <- function(x, language = get_locale(), ...) {
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#' @rdname mo_property
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#' @export
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mo_synonyms <- function(x, ...) {
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x <- AMR::as.mo(x, ...)
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x <- as.mo(x, ...)
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metadata <- get_mo_failures_uncertainties_renamed()
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IDs <- AMR::mo_property(x = x, property = "col_id", language = NULL)
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IDs <- mo_property(x = x, property = "col_id", language = NULL)
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syns <- lapply(IDs, function(col_id) {
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res <- sort(AMR::microorganisms.old[which(AMR::microorganisms.old$col_id_new == col_id), "fullname"])
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res <- sort(microorganisms.old[which(microorganisms.old$col_id_new == col_id), "fullname"])
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if (length(res) == 0) {
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NULL
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} else {
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@ -335,7 +335,7 @@ mo_synonyms <- function(x, ...) {
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#' @rdname mo_property
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#' @export
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mo_info <- function(x, language = get_locale(), ...) {
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x <- AMR::as.mo(x, ...)
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x <- as.mo(x, ...)
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metadata <- get_mo_failures_uncertainties_renamed()
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info <- lapply(x, function(y)
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@ -360,12 +360,12 @@ mo_info <- function(x, language = get_locale(), ...) {
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#' @importFrom dplyr %>% left_join select mutate case_when
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#' @export
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mo_url <- function(x, open = FALSE, ...) {
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mo <- AMR::as.mo(x = x, ... = ...)
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mo_names <- AMR::mo_name(mo)
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mo <- as.mo(x = x, ... = ...)
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mo_names <- mo_name(mo)
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metadata <- get_mo_failures_uncertainties_renamed()
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df <- data.frame(mo, stringsAsFactors = FALSE) %>%
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left_join(select(AMR::microorganisms, mo, source, species_id), by = "mo") %>%
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left_join(select(microorganisms, mo, source, species_id), by = "mo") %>%
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mutate(url = case_when(source == "CoL" ~
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paste0(gsub("{year}", catalogue_of_life$year, catalogue_of_life$url_CoL, fixed = TRUE), "details/species/id/", species_id),
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source == "DSMZ" ~
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@ -394,7 +394,7 @@ mo_property <- function(x, property = "fullname", language = get_locale(), ...)
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if (length(property) != 1L) {
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stop("'property' must be of length 1.")
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}
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if (!property %in% colnames(AMR::microorganisms)) {
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if (!property %in% colnames(microorganisms)) {
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stop("invalid property: '", property, "' - use a column name of the `microorganisms` data set")
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}
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@ -403,7 +403,7 @@ mo_property <- function(x, property = "fullname", language = get_locale(), ...)
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mo_validate <- function(x, property, ...) {
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load_AMR_package()
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check_dataset_integrity()
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dots <- list(...)
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Becker <- dots$Becker
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@ -417,7 +417,7 @@ mo_validate <- function(x, property, ...) {
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# try to catch an error when inputting an invalid parameter
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# so the 'call.' can be set to FALSE
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tryCatch(x[1L] %in% AMR::microorganisms[1, property],
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tryCatch(x[1L] %in% microorganisms[1, property],
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error = function(e) stop(e$message, call. = FALSE))
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if (is.mo(x)
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@ -426,7 +426,7 @@ mo_validate <- function(x, property, ...) {
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# this will not reset mo_uncertainties and mo_failures
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# because it's already a valid MO
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x <- exec_as.mo(x, property = property, initial_search = FALSE, ...)
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} else if (!all(x %in% pull(AMR::microorganisms, property))
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} else if (!all(x %in% pull(microorganisms, property))
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| Becker %in% c(TRUE, "all")
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x <- exec_as.mo(x, property = property, ...)
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