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(v1.2.0.9034) code cleaning

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dr. M.S. (Matthijs) Berends
2020-07-13 09:17:24 +02:00
parent c0cf7ab02b
commit 6ab468362d
36 changed files with 266 additions and 265 deletions
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46
R/mo_property.R
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@ -151,9 +151,9 @@ mo_fullname <- mo_name
#' @export
mo_shortname <- function(x, language = get_locale(), ...) {
x.mo <- as.mo(x, ...)
metadata <- get_mo_failures_uncertainties_renamed()
replace_empty <- function(x) {
x[x == ""] <- "spp."
x
@ -161,13 +161,13 @@ mo_shortname <- function(x, language = get_locale(), ...) {
# get first char of genus and complete species in English
shortnames <- paste0(substr(mo_genus(x.mo, language = NULL), 1, 1), ". ", replace_empty(mo_species(x.mo, language = NULL)))
# exceptions for Staphylococci
shortnames[shortnames == "S. coagulase-negative"] <- "CoNS"
shortnames[shortnames == "S. coagulase-positive"] <- "CoPS"
# exceptions for Streptococci: Streptococcus Group A -> GAS
shortnames[shortnames %like% "S. group [ABCDFGHK]"] <- paste0("G", gsub("S. group ([ABCDFGHK])", "\\1", shortnames[shortnames %like% "S. group [ABCDFGHK]"]), "S")
load_mo_failures_uncertainties_renamed(metadata)
translate_AMR(shortnames, language = language, only_unknown = FALSE)
}
@ -235,7 +235,7 @@ mo_type <- function(x, language = get_locale(), ...) {
mo_gramstain <- function(x, language = get_locale(), ...) {
x.mo <- as.mo(x, ...)
metadata <- get_mo_failures_uncertainties_renamed()
x.phylum <- mo_phylum(x.mo)
# DETERMINE GRAM STAIN FOR BACTERIA
# Source: https://itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=956097
@ -256,7 +256,7 @@ mo_gramstain <- function(x, language = get_locale(), ...) {
"Firmicutes",
"Tenericutes")
| x.mo == "B_GRAMP"] <- "Gram-positive"
load_mo_failures_uncertainties_renamed(metadata)
translate_AMR(x, language = language, only_unknown = FALSE)
}
@ -302,16 +302,16 @@ mo_rank <- function(x, ...) {
mo_taxonomy <- function(x, language = get_locale(), ...) {
x <- as.mo(x, ...)
metadata <- get_mo_failures_uncertainties_renamed()
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))
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
}
@ -321,7 +321,7 @@ mo_taxonomy <- function(x, language = get_locale(), ...) {
mo_synonyms <- function(x, ...) {
x <- as.mo(x, ...)
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$fullname_new == newname), "fullname"])
@ -337,7 +337,7 @@ mo_synonyms <- function(x, ...) {
} else {
result <- unlist(syns)
}
load_mo_failures_uncertainties_renamed(metadata)
result
}
@ -347,7 +347,7 @@ mo_synonyms <- function(x, ...) {
mo_info <- function(x, language = get_locale(), ...) {
x <- as.mo(x, ...)
metadata <- get_mo_failures_uncertainties_renamed()
info <- lapply(x, function(y)
c(mo_taxonomy(y, language = language),
list(synonyms = mo_synonyms(y),
@ -360,7 +360,7 @@ mo_info <- function(x, language = get_locale(), ...) {
} else {
result <- info[[1L]]
}
load_mo_failures_uncertainties_renamed(metadata)
result
}
@ -388,7 +388,7 @@ mo_url <- function(x, open = FALSE, ...) {
}
utils::browseURL(u[1L])
}
load_mo_failures_uncertainties_renamed(metadata)
u
}
@ -400,14 +400,14 @@ mo_property <- function(x, property = "fullname", language = get_locale(), ...)
stop_ifnot(length(property) == 1L, "'property' must be of length 1")
stop_ifnot(property %in% colnames(microorganisms),
"invalid property: '", property, "' - use a column name of the `microorganisms` data set")
translate_AMR(mo_validate(x = x, property = property, ...), language = language, only_unknown = TRUE)
}
mo_validate <- function(x, property, ...) {
check_dataset_integrity()
dots <- list(...)
Becker <- dots$Becker
if (is.null(Becker)) {
@ -417,7 +417,7 @@ mo_validate <- function(x, property, ...) {
if (is.null(Lancefield)) {
Lancefield <- FALSE
}
# try to catch an error when inputting an invalid parameter
# so the 'call.' can be set to FALSE
tryCatch(x[1L] %in% MO_lookup[1, property, drop = TRUE],