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(v0.9.0.9023) EUCAST 2020 guidelines

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dr. M.S. (Matthijs) Berends
2020-02-14 19:54:13 +01:00
parent 5a98e6b777
commit 9b8b02960e
43 changed files with 16588 additions and 14564 deletions
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44
R/mo_property.R
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@ -145,7 +145,7 @@ mo_fullname <- mo_name
#' @rdname mo_property
#' @export
mo_shortname <- function(x, language = get_locale(), ...) {
x.mo <- AMR::as.mo(x, ...)
x.mo <- as.mo(x, ...)
metadata <- get_mo_failures_uncertainties_renamed()
replace_empty <- function(x) {
@ -223,7 +223,7 @@ mo_type <- function(x, language = get_locale(), ...) {
#' @rdname mo_property
#' @export
mo_gramstain <- function(x, language = get_locale(), ...) {
x.mo <- AMR::as.mo(x, ...)
x.mo <- as.mo(x, ...)
metadata <- get_mo_failures_uncertainties_renamed()
x.phylum <- mo_phylum(x.mo)
@ -290,17 +290,17 @@ mo_rank <- function(x, ...) {
#' @rdname mo_property
#' @export
mo_taxonomy <- function(x, language = get_locale(), ...) {
x <- AMR::as.mo(x, ...)
x <- as.mo(x, ...)
metadata <- get_mo_failures_uncertainties_renamed()
result <- base::list(kingdom = AMR::mo_kingdom(x, language = language),
phylum = AMR::mo_phylum(x, language = language),
class = AMR::mo_class(x, language = language),
order = AMR::mo_order(x, language = language),
family = AMR::mo_family(x, language = language),
genus = AMR::mo_genus(x, language = language),
species = AMR::mo_species(x, language = language),
subspecies = AMR::mo_subspecies(x, language = language))
result <- base::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)
result
@ -309,12 +309,12 @@ mo_taxonomy <- function(x, language = get_locale(), ...) {
#' @rdname mo_property
#' @export
mo_synonyms <- function(x, ...) {
x <- AMR::as.mo(x, ...)
x <- as.mo(x, ...)
metadata <- get_mo_failures_uncertainties_renamed()
IDs <- AMR::mo_property(x = x, property = "col_id", language = NULL)
IDs <- mo_property(x = x, property = "col_id", language = NULL)
syns <- lapply(IDs, function(col_id) {
res <- sort(AMR::microorganisms.old[which(AMR::microorganisms.old$col_id_new == col_id), "fullname"])
res <- sort(microorganisms.old[which(microorganisms.old$col_id_new == col_id), "fullname"])
if (length(res) == 0) {
NULL
} else {
@ -335,7 +335,7 @@ mo_synonyms <- function(x, ...) {
#' @rdname mo_property
#' @export
mo_info <- function(x, language = get_locale(), ...) {
x <- AMR::as.mo(x, ...)
x <- as.mo(x, ...)
metadata <- get_mo_failures_uncertainties_renamed()
info <- lapply(x, function(y)
@ -360,12 +360,12 @@ mo_info <- function(x, language = get_locale(), ...) {
#' @importFrom dplyr %>% left_join select mutate case_when
#' @export
mo_url <- function(x, open = FALSE, ...) {
mo <- AMR::as.mo(x = x, ... = ...)
mo_names <- AMR::mo_name(mo)
mo <- as.mo(x = x, ... = ...)
mo_names <- mo_name(mo)
metadata <- get_mo_failures_uncertainties_renamed()
df <- data.frame(mo, stringsAsFactors = FALSE) %>%
left_join(select(AMR::microorganisms, mo, source, species_id), by = "mo") %>%
left_join(select(microorganisms, mo, source, species_id), by = "mo") %>%
mutate(url = case_when(source == "CoL" ~
paste0(gsub("{year}", catalogue_of_life$year, catalogue_of_life$url_CoL, fixed = TRUE), "details/species/id/", species_id),
source == "DSMZ" ~
@ -394,7 +394,7 @@ mo_property <- function(x, property = "fullname", language = get_locale(), ...)
if (length(property) != 1L) {
stop("'property' must be of length 1.")
}
if (!property %in% colnames(AMR::microorganisms)) {
if (!property %in% colnames(microorganisms)) {
stop("invalid property: '", property, "' - use a column name of the `microorganisms` data set")
}
@ -403,7 +403,7 @@ mo_property <- function(x, property = "fullname", language = get_locale(), ...)
mo_validate <- function(x, property, ...) {
load_AMR_package()
check_dataset_integrity()
dots <- list(...)
Becker <- dots$Becker
@ -417,7 +417,7 @@ mo_validate <- function(x, property, ...) {
# try to catch an error when inputting an invalid parameter
# so the 'call.' can be set to FALSE
tryCatch(x[1L] %in% AMR::microorganisms[1, property],
tryCatch(x[1L] %in% microorganisms[1, property],
error = function(e) stop(e$message, call. = FALSE))
if (is.mo(x)
@ -426,7 +426,7 @@ mo_validate <- function(x, property, ...) {
# this will not reset mo_uncertainties and mo_failures
# because it's already a valid MO
x <- exec_as.mo(x, property = property, initial_search = FALSE, ...)
} else if (!all(x %in% pull(AMR::microorganisms, property))
} else if (!all(x %in% pull(microorganisms, property))
| Becker %in% c(TRUE, "all")
| Lancefield %in% c(TRUE, "all")) {
x <- exec_as.mo(x, property = property, ...)