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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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30
R/mo.R
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@ -175,7 +175,7 @@ as.mo <- function(x,
reference_df = get_mo_source(),
...) {
load_AMR_package()
check_dataset_integrity()
# WHONET: xxx = no growth
x[tolower(as.character(paste0(x, ""))) %in% c("", "xxx", "na", "nan")] <- NA_character_
@ -238,7 +238,7 @@ is.mo <- function(x) {
#' @importFrom data.table data.table as.data.table setkey
#' @importFrom crayon magenta red blue silver italic
#' @importFrom cleaner percentage
# param property a column name of AMR::microorganisms
# param property a column name of microorganisms
# param initial_search logical - is FALSE when coming from uncertain tries, which uses exec_as.mo internally too
# param dyslexia_mode logical - also check for characters that resemble others
# param debug logical - show different lookup texts while searching
@ -254,7 +254,7 @@ exec_as.mo <- function(x,
debug = FALSE,
reference_data_to_use = microorganismsDT) {
load_AMR_package()
check_dataset_integrity()
# WHONET: xxx = no growth
x[tolower(as.character(paste0(x, ""))) %in% c("", "xxx", "na", "nan")] <- NA_character_
@ -365,7 +365,7 @@ exec_as.mo <- function(x,
suppressWarnings(
x <- data.frame(x = x, stringsAsFactors = FALSE) %>%
left_join(reference_df, by = "x") %>%
left_join(AMR::microorganisms, by = "mo") %>%
left_join(microorganisms, by = "mo") %>%
pull(property)
)
@ -393,9 +393,9 @@ exec_as.mo <- function(x,
on = "fullname_lower",
..property][[1]]
} else if (all(toupper(x) %in% AMR::microorganisms.codes$code)) {
} else if (all(toupper(x) %in% microorganisms.codes$code)) {
# commonly used MO codes
y <- as.data.table(AMR::microorganisms.codes)[data.table(code = toupper(x)),
y <- as.data.table(microorganisms.codes)[data.table(code = toupper(x)),
on = "code", ]
x <- reference_data_to_use[data.table(mo = y[["mo"]]),
@ -412,7 +412,7 @@ exec_as.mo <- function(x,
..property][[1]]
x <- y
} else if (!all(x %in% AMR::microorganisms[, property])) {
} else if (!all(x %in% microorganisms[, property])) {
strip_whitespace <- function(x, dyslexia_mode) {
# all whitespaces (tab, new lines, etc.) should be one space
@ -632,8 +632,8 @@ exec_as.mo <- function(x,
}
# WHONET and other common LIS codes
if (any(toupper(c(x_backup[i], x_backup_without_spp[i])) %in% AMR::microorganisms.codes$code)) {
mo_found <- AMR::microorganisms.codes[which(AMR::microorganisms.codes$code %in% toupper(c(x_backup[i], x_backup_without_spp[i]))), "mo"][1L]
if (any(toupper(c(x_backup[i], x_backup_without_spp[i])) %in% microorganisms.codes$code)) {
mo_found <- microorganisms.codes[which(microorganisms.codes$code %in% toupper(c(x_backup[i], x_backup_without_spp[i]))), "mo"][1L]
if (length(mo_found) > 0) {
x[i] <- microorganismsDT[mo == mo_found,
..property][[1]][1L]
@ -1476,8 +1476,7 @@ exec_as.mo <- function(x,
msg <- paste0(msg, ": ", paste('"', unique(failures), '"', sep = "", collapse = ", "))
}
msg <- paste0(msg, ". Use mo_failures() to review ", plural[2], ". Edit the `allow_uncertain` parameter if needed (see ?as.mo).")
cat("\n")
warning(red(msg),
warning(red(paste0("\n", msg)),
call. = FALSE,
immediate. = TRUE) # thus will always be shown, even if >= warnings
}
@ -1491,8 +1490,7 @@ exec_as.mo <- function(x,
}
msg <- paste0("Result", plural[1], " of ", nr2char(NROW(uncertainties)), " value", plural[1],
" ", plural[3], " guessed with uncertainty. Use mo_uncertainties() to review ", plural[2], ".")
cat("\n")
warning(red(msg),
warning(red(paste0("\n", msg)),
call. = FALSE,
immediate. = TRUE) # thus will always be shown, even if >= warnings
}
@ -1753,7 +1751,7 @@ as.data.frame.mo <- function(x, ...) {
"[<-.mo" <- function(i, j, ..., value) {
y <- NextMethod()
attributes(y) <- attributes(i)
class_integrity_check(y, "microorganism code", c(as.character(AMR::microorganisms$mo),
class_integrity_check(y, "microorganism code", c(as.character(microorganisms$mo),
as.character(microorganisms.translation$mo_old)))
}
#' @exportMethod [[<-.mo
@ -1762,7 +1760,7 @@ as.data.frame.mo <- function(x, ...) {
"[[<-.mo" <- function(i, j, ..., value) {
y <- NextMethod()
attributes(y) <- attributes(i)
class_integrity_check(y, "microorganism code", c(as.character(AMR::microorganisms$mo),
class_integrity_check(y, "microorganism code", c(as.character(microorganisms$mo),
as.character(microorganisms.translation$mo_old)))
}
#' @exportMethod c.mo
@ -1771,7 +1769,7 @@ as.data.frame.mo <- function(x, ...) {
c.mo <- function(x, ...) {
y <- NextMethod()
attributes(y) <- attributes(x)
class_integrity_check(y, "microorganism code", c(as.character(AMR::microorganisms$mo),
class_integrity_check(y, "microorganism code", c(as.character(microorganisms$mo),
as.character(microorganisms.translation$mo_old)))
}